cor.mtest function How to Combining correlogram with the significance test of two different vectors?

Hello everyone, I am having problems with the cor.mtest function. Is it possible to obtain the level of significance of two different set of variables, and then eliminate those that are below 0.05 (p-value) from the correlation graph?

This is what I tried to do.

library(tidyverse)
library(corrplot)
#> corrplot 0.84 loaded
library(corrr)

metadata <- data.frame(tibble::tribble(
                          ~SampleID,  ~DO,   ~pH, ~Temp, ~Turbidity,  ~ORP, ~NH4, ~NO3,   ~BGA, ~Chlrophyll,   ~CE,
                               "1A", 4.24,  9.94, 24.48,       87.3,    97, 4.46,  3.6, 279133,        36.6, 1.074,
                               "1B", 2.58, 10.06, 24.95,       95.2, 108.4, 4.62, 3.98, 279113,        38.9, 1.082,
                               "1C", 2.85,  9.98, 24.01,       98.8, 102.9, 4.37, 3.57, 265304,          40, 1.081,
                               "1D", 3.81,  9.07, 26.67,       24.9,    94,  5.6, 3.53,  11603,          44, 1.147,
                               "1E", 2.64,  8.99, 24.01,       43.1,  63.9, 3.38, 2.55, 218471,          35, 1.156,
                               "1F", 4.61,  8.93,  23.5,       49.1,  64.7, 3.21, 2.28, 226658,        32.8, 1.157,
                               "1G", 5.74,  9.24, 24.46,       68.6,  40.3, 1.93, 0.71, 267389,          44, 1.072,
                               "1H", 3.69,  9.32, 24.65,       69.8,  48.1, 2.21,  1.2, 267144,        44.8, 1.152,
                               "2A", 4.24,  9.94, 24.48,       87.3,    97, 4.46,  3.6, 279133,        36.6, 1.074,
                               "2B", 2.66,    10, 24.92,        113, 111.9, 4.75, 3.21, 270193,        39.8, 1.081,
                               "2C", 2.85,  9.98, 24.01,       98.8, 102.9, 4.37, 3.57, 265304,          40, 1.081,
                               "2D", 3.81,  9.07, 26.67,       24.9,    94,  5.6, 3.53,  11603,          44, 1.147,
                               "2E", 2.64,  8.99, 24.01,       43.1,  63.9, 3.38, 2.55, 218471,          35, 1.156,
                               "2F", 4.61,  8.93,  23.5,       49.1,  64.7, 3.21, 2.28, 226658,        32.8, 1.157,
                               "2G", 5.74,  9.24, 24.46,       68.6,  40.3, 1.93, 0.71, 267389,          44, 1.072,
                               "2H", 3.69,  9.32, 24.65,       69.8,  48.1, 2.21,  1.2, 267144,        44.8, 1.152,
                               "3A", 2.51, 10.04, 24.35,       87.7,  91.3,  4.5, 3.36, 267716,        39.6, 1.075,
                               "3B", 2.66,    10, 24.92,        113, 111.9, 4.75, 3.21, 270193,        39.8, 1.081,
                               "3C", 3.14,    10,    24,       96.9,   108, 4.48, 3.76, 279119,        38.5,  1.08,
                               "3D", 2.92,  9.06, 26.46,       39.7,  23.7, 7.64, 3.66,  66608,        45.1, 1.138,
                               "3E", 1.83,  8.99, 23.99,         49,  64.1, 3.18, 2.44, 213497,        42.2, 1.155,
                               "3F", 1.82,  8.92, 23.43,       47.6,  60.4, 3.09, 2.06, 242331,        50.2, 1.157,
                               "3G", 3.02,  9.18, 24.14,       66.6,  40.6, 2.19, 0.67, 267007,        43.6, 1.061,
                               "4A", 2.51, 10.04, 24.35,       87.7,  91.3,  4.5, 3.36, 267716,        39.6, 1.075,
                               "4B", 3.04,  9.96, 24.04,       98.5,  98.9, 3.97, 4.35, 279109,          43, 1.083,
                               "4C", 2.85,  9.98, 24.01,       98.8, 102.9, 4.37, 3.57, 265304,          40, 1.081,
                               "4D", 2.92,  9.06, 26.46,       39.7,  23.7, 7.64, 3.66,  66608,        45.1, 1.138,
                               "4E", 1.83,  8.99, 23.99,         49,  64.1, 3.18, 2.44, 213497,        42.2, 1.155,
                               "4F", 1.82,  8.92, 23.43,       47.6,  60.4, 3.09, 2.06, 242331,        50.2, 1.157,
                               "4G", 3.02,  9.18, 24.14,       66.6,  40.6, 2.19, 0.67, 267007,        43.6, 1.061,
                               "4H",  3.3,  9.32, 24.67,       74.1,  49.8, 2.14, 0.87, 261363,        45.1, 1.142,
                               "5A", 4.24,  9.94, 24.48,       87.3,    97, 4.46,  3.6, 279133,        36.6, 1.074,
                               "5B", 3.04,  9.96, 24.04,       98.5,  98.9, 3.97, 4.35, 279109,          43, 1.083,
                               "5D", 3.81,  9.07, 26.67,       24.9,    94,  5.6, 3.53,  11603,          44, 1.147,
                               "5E", 2.64,  8.99, 24.01,       43.1,  63.9, 3.38, 2.55, 218471,          35, 1.156,
                               "5F", 4.61,  8.93,  23.5,       49.1,  64.7, 3.21, 2.28, 226658,        32.8, 1.157,
                               "5G", 5.74,  9.24, 24.46,       68.6,  40.3, 1.93, 0.71, 267389,          44, 1.072,
                               "5H", 3.69,  9.32, 24.65,       69.8,  48.1, 2.21,  1.2, 267144,        44.8, 1.152,
                               "6A", 4.24,  9.94, 24.48,       87.3,    97, 4.46,  3.6, 279133,        36.6, 1.074,
                               "6B", 2.09,  9.95, 24.01,       95.9,  92.8, 4.06, 3.68, 279100,          50, 1.077,
                               "6C", 2.98, 10.09, 24.36,       97.2, 106.9, 4.43, 3.34, 279099,          43, 1.077,
                               "6D", 3.81,  9.07, 26.67,       24.9,    94,  5.6, 3.53,  11603,          44, 1.147,
                               "6E", 1.83,  8.99, 23.99,         49,  64.1, 3.18, 2.44, 213497,        42.2, 1.155,
                               "6F", 1.82,  8.92, 23.43,       47.6,  60.4, 3.09, 2.06, 242331,        50.2, 1.157,
                               "6G", 3.02,  9.18, 24.14,       66.6,  40.6, 2.19, 0.67, 267007,        43.6, 1.061,
                               "6H",  3.3,  9.32, 24.67,       74.1,  49.8, 2.14, 0.87, 261363,        45.1, 1.142,
                               "7A", 2.51, 10.04, 24.35,       87.7,  91.3,  4.5, 3.36, 267716,        39.6, 1.075,
                               "7B", 2.09,  9.95, 24.01,       95.9,  92.8, 4.06, 3.68, 279100,          50, 1.081,
                               "7C", 2.98, 10.09, 24.36,       97.2, 106.9, 4.43, 3.34, 279099,          43, 1.077,
                               "7D", 8.17,  9.04, 24.88,       46.9,  90.4, 2.81, 2.25, 246979,          34, 1.154,
                               "7E", 2.63,     9,  24.7,       37.2,  74.9,  4.2, 2.99, 169175,        38.4, 1.179,
                               "7F", 7.69,  9.53, 26.14,       74.2,  67.7,  4.5,  1.3, 272332,        58.5, 1.072,
                               "7G", 3.07,  9.31, 24.19,       69.9,    42, 1.99, 0.74, 269519,        44.3, 1.152,
                               "7H",  3.7,  9.14, 22.65,       71.3,  37.1, 2.07, 0.68, 272096,          40, 1.127,
                               "8A", 2.51, 10.04, 24.35,       87.7,  91.3,  4.5, 3.36, 267716,        39.6, 1.075,
                               "8B", 3.04,  9.96, 24.04,       98.5,  98.9, 3.97, 4.35, 279109,          43, 1.083,
                               "8C", 2.18,  9.97,  24.4,      100.6, 102.7, 5.47, 4.11, 278137,        53.8, 1.078,
                               "8D", 8.17,  9.04, 24.88,       46.9,  90.4, 2.81, 2.25, 246979,          34, 1.154,
                               "8E", 2.63,     9,  24.7,       37.2,  74.9,  4.2, 2.99, 169175,        38.4, 1.179,
                               "8F", 7.69,  9.53, 26.14,       74.2,  67.7,  4.5,  1.3, 272332,        58.5, 1.072,
                               "8G", 3.07,  9.31, 24.19,       69.9,    42, 1.99, 0.74, 269519,        44.3, 1.152,
                               "8H",  3.7,  9.14, 22.65,       71.3,  37.1, 2.07, 0.68, 272096,          40, 1.127,
                               "9A", 2.58, 10.06, 24.95,       95.2, 108.4, 4.62, 3.98, 279113,        38.9, 1.082,
                               "9B", 2.09,  9.95, 24.01,       95.9,  92.8, 4.06, 3.68, 279100,          50, 1.081,
                               "9C", 2.18,  9.97,  24.4,      100.6, 102.7, 5.47, 4.11, 278137,        53.8, 1.078,
                               "9D", 2.16,  8.96,  24.3,         42,    53, 3.19,  2.1, 174271,        50.3, 1.161,
                               "9E",  1.7,  9.02, 24.72,       36.1,  63.4, 3.97, 2.55, 159046,        55.9,  1.69,
                               "9F",  6.8,  9.51, 26.15,       74.4,  73.9,  3.3, 1.11, 271503,        51.3, 1.061,
                               "9G", 1.95,  9.39,  23.9,       44.4,    42, 3.38, 0.69, 261124,        68.2, 1.147,
                               "9H", 4.28,  8.85, 20.65,       71.3,  37.5, 1.18, 0.69, 271303,        34.2, 1.102,
                              "10A", 2.58, 10.06, 24.95,       95.2, 108.4, 4.62, 3.98, 279113,        38.9, 1.082,
                              "10B", 2.09,  9.95, 24.01,       95.9,  92.8, 4.06, 3.68, 279100,          50, 1.081,
                              "10C", 2.98, 10.09, 24.36,       97.2, 106.9, 4.43, 3.34, 279099,          43, 1.077,
                              "10D", 2.16,  8.96,  24.3,         42,    53, 3.19,  2.1, 174271,        50.3, 1.161,
                              "10E",  1.7,  9.02, 24.72,       36.1,  63.4, 3.97, 2.55, 159046,        55.9,  1.69,
                              "10F",  6.8,  9.51, 26.15,       74.4,  73.9,  3.3, 1.11, 271503,        51.3, 1.061,
                              "10G", 1.95,  9.39,  23.9,       44.4,    42, 3.38, 0.69, 261124,        68.2, 1.147,
                              "10H", 4.28,  8.85, 20.65,       71.3,  37.5, 1.18, 0.69, 271303,        34.2, 1.102,
                              "11A", 2.66,    10, 24.92,        113, 111.9, 4.75, 3.21, 270193,        39.8, 1.081,
                              "11B", 3.14,    10,    24,       96.9,   108, 4.48, 3.76, 279119,        38.5,  1.08,
                              "11C", 2.18,  9.97,  24.4,      100.6, 102.7, 5.47, 4.11, 278137,        53.8, 1.078,
                              "11D", 8.17,  9.04, 24.88,       46.9,  90.4, 2.81, 2.25, 246979,          34, 1.154,
                              "11E", 2.63,     9,  24.7,       37.2,  74.9,  4.2, 2.99, 169175,        38.4, 1.179,
                              "11F", 7.69,  9.53, 26.14,       74.2,  67.7,  4.5,  1.3, 272332,        58.5, 1.072,
                              "11G", 3.07,  9.31, 24.19,       69.9,    42, 1.99, 0.74, 269519,        44.3, 1.152,
                              "11H",  3.7,  9.14, 22.65,       71.3,  37.1, 2.07, 0.68, 272096,          40, 1.127,
                              "12A", 2.66,    10, 24.92,        113, 111.9, 4.75, 3.21, 270193,        39.8, 1.081,
                              "12B", 3.14,    10,    24,       96.9, 111.9, 4.48, 3.76, 279119,        38.5,  1.08,
                              "12C", 2.92,  9.06, 26.46,       39.7,  23.7, 7.64, 3.66,  66608,        45.1, 1.138,
                              "12D", 2.16,  8.96,  24.3,         42,    53, 3.19,  2.1, 174271,        50.3, 1.161,
                              "12E",  1.7,  9.02, 24.72,       36.1,  63.4, 3.97, 2.55, 159046,        55.9,  1.69,
                              "12F",  6.8,  9.51, 26.15,       74.4,  73.9,  3.3, 1.11, 271503,        51.3, 1.061,
                              "12G", 1.95,  9.39,  23.9,       44.4,    42, 3.38, 0.69, 261124,        68.2, 1.147,
                              "12H", 4.28,  8.85, 20.65,       71.3,  37.5, 1.18, 0.69, 271303,        34.2, 1.102
                          )
)

bacteria <- data.frame (tibble::tribble(
                           ~index, ~Cylindrospermopsis, ~Un.Nostocaceae, ~Planktothrix, ~Un.Nostocales, ~Phormidesmis, ~Un.Cyanobiaceae, ~Un.Oxyphotobacteria, ~Un.Cyanobacteria,
                             "1A",                   0,               0,             0,             12,            66,                0,                 7137,              1467,
                             "1B",                   0,               0,             0,              6,            35,                0,                 5549,               238,
                             "1C",                   0,              19,             2,              0,            96,                0,                 1861,               708,
                             "1D",                   0,               0,             0,              0,            66,               19,                 3185,              4001,
                             "1E",                   0,            1662,             0,            207,           720,              529,                 7468,              1928,
                             "1F",                   0,            2090,             0,            425,           432,                6,                18421,              4460,
                             "1G",                   0,             372,             0,              0,            19,                2,                 4191,               361,
                             "1H",                   0,             433,           613,             46,          1215,                0,                12240,              1970,
                             "2A",                   0,            1000,             0,              8,           195,                0,                20728,              4350,
                             "2B",                   0,             769,            35,             62,            46,              619,                13438,              3076,
                             "2C",                   0,             639,             0,             31,            14,               21,                17664,              2008,
                             "2D",                   0,             510,             0,              0,            58,                0,                 5085,              2745,
                             "2E",                   0,             319,             0,              0,            60,              200,                 8376,              1613,
                             "2F",                   0,             501,             2,             89,           807,                0,                 8906,               983,
                             "2G",                   0,             930,             0,            115,           141,              195,                13273,              1514,
                             "2H",                   9,            1867,            18,            535,           279,               26,                18506,              3531,
                             "3A",                  44,             272,            88,              3,          1139,                0,                 7959,              1700,
                             "3B",                 570,              43,            60,             22,            65,                3,                  762,               367,
                             "3C",                   0,               0,             0,              0,           173,                0,                 3088,                45,
                             "3D",                   0,               0,             0,              0,             0,               52,                 3009,              1683,
                             "3E",                   0,            1039,             0,            199,            74,                0,                 4120,               754,
                             "3F",                   0,             388,             0,             10,           318,                0,                 5083,               675,
                             "3G",                   0,             982,             0,            298,           407,                0,                 5573,              1031,
                             "4A",                   0,            3272,             0,            578,           558,               32,                24267,              9707,
                             "4B",                   0,             895,             0,             60,            33,             1685,                16403,              3105,
                             "4C",                   0,             243,             0,              0,             0,               57,                 6043,               570,
                             "4D",                   0,            1621,             0,            148,            15,                6,                 8472,              2357,
                             "4E",                   0,            1094,             0,            168,           165,                0,                 8351,              2424,
                             "4F",                   0,              43,             0,              0,           302,                0,                  491,               570,
                             "4G",                   0,             291,             0,             74,           152,              359,                13031,              3066,
                             "4H",                  16,            2814,            28,            616,          1841,                0,                33094,              6509,
                             "5A",                   0,               2,             0,            111,             2,               58,                11083,              4240,
                             "5B",                   0,               0,             0,              0,           108,                0,                 4248,               676,
                             "5D",                   0,            1006,             0,            214,           285,                0,                 8839,              1176,
                             "5E",                   0,               2,            17,            120,           355,               19,                10286,               213,
                             "5F",                   0,            1051,             2,            158,           583,                0,                14778,              1765,
                             "5G",                   2,            1040,            28,            587,             9,              355,                 3584,              1574,
                             "5H",                   0,             244,             0,             70,            55,               22,                10905,              7012,
                             "6A",                  37,            1221,             0,            126,            43,              473,                22140,              5237,
                             "6B",                   0,            1190,             0,             92,           140,              599,                22958,              3646,
                             "6C",                   0,             266,             0,              0,            46,                0,                 5937,              1510,
                             "6D",                   0,              63,             0,              7,             0,                0,                 8240,               900,
                             "6E",                   0,            1016,             0,            201,           130,                0,                 6252,              1583,
                             "6F",                   0,            2226,             0,            491,           190,                0,                15494,              3392,
                             "6G",                   0,             206,             0,            296,             8,              205,                 9631,              5514,
                             "6H",                   0,            2014,           123,            430,          3015,               74,                40839,              7004,
                             "7A",                   0,             183,             0,             16,           172,               50,                 7201,              4795,
                             "7B",                   0,               0,             0,              0,             0,                0,                 2146,               732,
                             "7C",                   0,              27,             0,              0,             0,                0,                 3927,               450,
                             "7D",                   0,             139,           128,             42,            97,               11,                26197,              1932,
                             "7E",                   0,            1266,             0,            274,          1208,                0,                17161,              4310,
                             "7F",                   0,             232,           274,              3,           335,               60,                14640,               293,
                             "7G",                   0,            1036,             0,            210,             5,              424,                 1888,              1837,
                             "7H",                   0,             102,             0,              0,             0,                0,                 2860,              2943,
                             "8A",                   0,            1096,             0,             83,            56,               16,                18949,              3364,
                             "8B",                   0,            2439,             0,            263,           117,               48,                30505,              6066,
                             "8C",                   0,              39,            29,              0,           102,                0,                10406,               572,
                             "8D",                   0,            2214,             0,            324,            97,                0,                14814,              8608,
                             "8E",                   0,            1709,           102,            323,             6,                0,                 7553,              2455,
                             "8F",                   0,            2633,             0,            237,           391,                0,                24075,              3692,
                             "8G",                  45,            2557,           442,            610,           108,             1817,                 7788,              4399,
                             "8H",                   0,            1403,            24,            251,           256,                4,                16103,              3045,
                             "9A",                   0,               2,             0,             20,             6,                0,                 3794,              1919,
                             "9B",                   0,               5,             0,             30,           483,                8,                 8916,              1307,
                             "9C",                   0,              46,             0,              0,             0,                0,                 2817,              1041,
                             "9D",                   0,            3157,             0,            706,           162,                0,                17692,              8381,
                             "9E",                   0,             342,           125,             64,          1240,              380,                20302,              2008,
                             "9F",                   8,            1023,             0,            257,           584,               12,                48687,              5115,
                             "9G",                   0,             407,             0,             72,            75,              195,                14834,              2512,
                             "9H",                3395,            2082,          2796,            357,           540,                0,                 4402,              1391,
                            "10A",                   0,             654,             0,             37,           116,              120,                14300,              3054,
                            "10B",                   0,             343,             0,              0,             0,               77,                15485,              1203,
                            "10C",                   0,             358,             0,              0,             0,                0,                 2695,              1719,
                            "10D",                   0,              38,            47,              0,            18,               37,                13401,               342,
                            "10E",                   0,            2265,             0,            382,            28,               15,                 9052,              2779,
                            "10F",                   0,             824,             0,            127,            76,                0,                13282,               743,
                            "10G",                   0,             338,            40,              5,           281,               13,                 2492,               939,
                            "10H",                   0,             151,             0,              0,            37,                0,                 2924,               700,
                            "11A",                   0,              11,             0,              0,             6,             2111,                  317,              1532,
                            "11B",                   0,              27,             0,              0,             0,                0,                  968,               702,
                            "11C",                   0,               0,             0,              0,            62,                9,                 4148,              2733,
                            "11D",                   0,            1108,             0,            211,           165,                0,                10756,              4030,
                            "11E",                   0,            1105,             0,            190,           304,                0,                10605,              1595,
                            "11F",                   0,               0,             0,             19,            70,               20,                 4327,               390,
                            "11G",                   0,               0,             0,             16,            54,               56,                 6701,              2077,
                            "11H",                   0,              88,             0,              0,            20,                0,                14377,              1305,
                            "12A",                   0,             441,             0,             50,           123,              115,                29898,              2216,
                            "12B",                   0,             404,             0,              0,            59,               55,                11845,              1397,
                            "12C",                   0,             623,             0,              6,            57,                0,                18824,              1992,
                            "12D",                  77,            3141,           145,            695,           172,              166,                 9555,              5101,
                            "12E",                   0,             172,             0,              0,            67,                5,                 6934,               243,
                            "12F",                   0,            2631,             0,            425,            74,               11,                16460,              2880,
                            "12G",                   2,            3522,           319,            784,           672,                0,                29848,              9140,
                            "12H",                 280,            1552,           216,            350,           551,               10,                33984,              7351
                           )
)
library(RColorBrewer)
res1 <- cor.mtest(bind_cols(bacteria[, -1],metadata[, -1]), conf.level = 0.95)

corrr::correlate(bind_cols(metadata[, -1], bacteria[, -1])) %>%
  filter(rowname %in% colnames(metadata)) %>%
  select(one_of(c("rowname", colnames(bacteria)[-1]))) %>%
  as.data.frame() %>%
  column_to_rownames("rowname") %>%
  as.matrix() %>%
  corrplot::corrplot(is.corr = FALSE, p.mat = res1$p, insig= "blank", sig.level = 0.05, tl.col = "black", tl.srt = 45,
                     col= brewer.pal (n=10, name= "PuOr"))
#> 
#> Correlation method: 'pearson'
#> Missing treated using: 'pairwise.complete.obs'

Created on 2019-11-04 by the reprex package (v0.3.0)

The graphic is wrong.

The example I found was this: https://cran.r-project.org/web/packages/corrplot/vignettes/corrplot-intro.html

Any help in getting a complete set of information would be greatly appreciated!

Greetings,

Osiris

You use filter() to remove the 8 rows that correspond to the bacteria and you use select() to remove the 10 columns that correspond to the metadata in the matrix returned by corrr::correlate(). You have to do the same in res1$p, an 18 x 18 matrix, where the first 8 rows and first 8 columns correspond to the bacteria and the remaining 10 of each correspond to the metadata. Notice how I trim res1$p when assigning a value to p.mat in the call to corrplot.

library(tidyverse)
#> Warning: package 'ggplot2' was built under R version 3.5.3
#> Warning: package 'tibble' was built under R version 3.5.3
#> Warning: package 'tidyr' was built under R version 3.5.3
#> Warning: package 'readr' was built under R version 3.5.3
#> Warning: package 'purrr' was built under R version 3.5.3
#> Warning: package 'dplyr' was built under R version 3.5.3
#> Warning: package 'stringr' was built under R version 3.5.3
#> Warning: package 'forcats' was built under R version 3.5.3
library(corrplot)
#> Warning: package 'corrplot' was built under R version 3.5.3
#> corrplot 0.84 loaded

library(corrr)
#> Warning: package 'corrr' was built under R version 3.5.3

metadata <- data.frame(tibble::tribble(
  ~SampleID,  ~DO,   ~pH, ~Temp, ~Turbidity,  ~ORP, ~NH4, ~NO3,   ~BGA, ~Chlrophyll,   ~CE,
  "1A", 4.24,  9.94, 24.48,       87.3,    97, 4.46,  3.6, 279133,        36.6, 1.074,
  "1B", 2.58, 10.06, 24.95,       95.2, 108.4, 4.62, 3.98, 279113,        38.9, 1.082,
  "1C", 2.85,  9.98, 24.01,       98.8, 102.9, 4.37, 3.57, 265304,          40, 1.081,
  "1D", 3.81,  9.07, 26.67,       24.9,    94,  5.6, 3.53,  11603,          44, 1.147,
  "1E", 2.64,  8.99, 24.01,       43.1,  63.9, 3.38, 2.55, 218471,          35, 1.156,
  "1F", 4.61,  8.93,  23.5,       49.1,  64.7, 3.21, 2.28, 226658,        32.8, 1.157,
  "1G", 5.74,  9.24, 24.46,       68.6,  40.3, 1.93, 0.71, 267389,          44, 1.072,
  "1H", 3.69,  9.32, 24.65,       69.8,  48.1, 2.21,  1.2, 267144,        44.8, 1.152,
  "2A", 4.24,  9.94, 24.48,       87.3,    97, 4.46,  3.6, 279133,        36.6, 1.074,
  "2B", 2.66,    10, 24.92,        113, 111.9, 4.75, 3.21, 270193,        39.8, 1.081,
  "2C", 2.85,  9.98, 24.01,       98.8, 102.9, 4.37, 3.57, 265304,          40, 1.081,
  "2D", 3.81,  9.07, 26.67,       24.9,    94,  5.6, 3.53,  11603,          44, 1.147,
  "2E", 2.64,  8.99, 24.01,       43.1,  63.9, 3.38, 2.55, 218471,          35, 1.156,
  "2F", 4.61,  8.93,  23.5,       49.1,  64.7, 3.21, 2.28, 226658,        32.8, 1.157,
  "2G", 5.74,  9.24, 24.46,       68.6,  40.3, 1.93, 0.71, 267389,          44, 1.072,
  "2H", 3.69,  9.32, 24.65,       69.8,  48.1, 2.21,  1.2, 267144,        44.8, 1.152,
  "3A", 2.51, 10.04, 24.35,       87.7,  91.3,  4.5, 3.36, 267716,        39.6, 1.075,
  "3B", 2.66,    10, 24.92,        113, 111.9, 4.75, 3.21, 270193,        39.8, 1.081,
  "3C", 3.14,    10,    24,       96.9,   108, 4.48, 3.76, 279119,        38.5,  1.08,
  "3D", 2.92,  9.06, 26.46,       39.7,  23.7, 7.64, 3.66,  66608,        45.1, 1.138,
  "3E", 1.83,  8.99, 23.99,         49,  64.1, 3.18, 2.44, 213497,        42.2, 1.155,
  "3F", 1.82,  8.92, 23.43,       47.6,  60.4, 3.09, 2.06, 242331,        50.2, 1.157,
  "3G", 3.02,  9.18, 24.14,       66.6,  40.6, 2.19, 0.67, 267007,        43.6, 1.061,
  "4A", 2.51, 10.04, 24.35,       87.7,  91.3,  4.5, 3.36, 267716,        39.6, 1.075,
  "4B", 3.04,  9.96, 24.04,       98.5,  98.9, 3.97, 4.35, 279109,          43, 1.083,
  "4C", 2.85,  9.98, 24.01,       98.8, 102.9, 4.37, 3.57, 265304,          40, 1.081,
  "4D", 2.92,  9.06, 26.46,       39.7,  23.7, 7.64, 3.66,  66608,        45.1, 1.138,
  "4E", 1.83,  8.99, 23.99,         49,  64.1, 3.18, 2.44, 213497,        42.2, 1.155,
  "4F", 1.82,  8.92, 23.43,       47.6,  60.4, 3.09, 2.06, 242331,        50.2, 1.157,
  "4G", 3.02,  9.18, 24.14,       66.6,  40.6, 2.19, 0.67, 267007,        43.6, 1.061,
  "4H",  3.3,  9.32, 24.67,       74.1,  49.8, 2.14, 0.87, 261363,        45.1, 1.142,
  "5A", 4.24,  9.94, 24.48,       87.3,    97, 4.46,  3.6, 279133,        36.6, 1.074,
  "5B", 3.04,  9.96, 24.04,       98.5,  98.9, 3.97, 4.35, 279109,          43, 1.083,
  "5D", 3.81,  9.07, 26.67,       24.9,    94,  5.6, 3.53,  11603,          44, 1.147,
  "5E", 2.64,  8.99, 24.01,       43.1,  63.9, 3.38, 2.55, 218471,          35, 1.156,
  "5F", 4.61,  8.93,  23.5,       49.1,  64.7, 3.21, 2.28, 226658,        32.8, 1.157,
  "5G", 5.74,  9.24, 24.46,       68.6,  40.3, 1.93, 0.71, 267389,          44, 1.072,
  "5H", 3.69,  9.32, 24.65,       69.8,  48.1, 2.21,  1.2, 267144,        44.8, 1.152,
  "6A", 4.24,  9.94, 24.48,       87.3,    97, 4.46,  3.6, 279133,        36.6, 1.074,
  "6B", 2.09,  9.95, 24.01,       95.9,  92.8, 4.06, 3.68, 279100,          50, 1.077,
  "6C", 2.98, 10.09, 24.36,       97.2, 106.9, 4.43, 3.34, 279099,          43, 1.077,
  "6D", 3.81,  9.07, 26.67,       24.9,    94,  5.6, 3.53,  11603,          44, 1.147,
  "6E", 1.83,  8.99, 23.99,         49,  64.1, 3.18, 2.44, 213497,        42.2, 1.155,
  "6F", 1.82,  8.92, 23.43,       47.6,  60.4, 3.09, 2.06, 242331,        50.2, 1.157,
  "6G", 3.02,  9.18, 24.14,       66.6,  40.6, 2.19, 0.67, 267007,        43.6, 1.061,
  "6H",  3.3,  9.32, 24.67,       74.1,  49.8, 2.14, 0.87, 261363,        45.1, 1.142,
  "7A", 2.51, 10.04, 24.35,       87.7,  91.3,  4.5, 3.36, 267716,        39.6, 1.075,
  "7B", 2.09,  9.95, 24.01,       95.9,  92.8, 4.06, 3.68, 279100,          50, 1.081,
  "7C", 2.98, 10.09, 24.36,       97.2, 106.9, 4.43, 3.34, 279099,          43, 1.077,
  "7D", 8.17,  9.04, 24.88,       46.9,  90.4, 2.81, 2.25, 246979,          34, 1.154,
  "7E", 2.63,     9,  24.7,       37.2,  74.9,  4.2, 2.99, 169175,        38.4, 1.179,
  "7F", 7.69,  9.53, 26.14,       74.2,  67.7,  4.5,  1.3, 272332,        58.5, 1.072,
  "7G", 3.07,  9.31, 24.19,       69.9,    42, 1.99, 0.74, 269519,        44.3, 1.152,
  "7H",  3.7,  9.14, 22.65,       71.3,  37.1, 2.07, 0.68, 272096,          40, 1.127,
  "8A", 2.51, 10.04, 24.35,       87.7,  91.3,  4.5, 3.36, 267716,        39.6, 1.075,
  "8B", 3.04,  9.96, 24.04,       98.5,  98.9, 3.97, 4.35, 279109,          43, 1.083,
  "8C", 2.18,  9.97,  24.4,      100.6, 102.7, 5.47, 4.11, 278137,        53.8, 1.078,
  "8D", 8.17,  9.04, 24.88,       46.9,  90.4, 2.81, 2.25, 246979,          34, 1.154,
  "8E", 2.63,     9,  24.7,       37.2,  74.9,  4.2, 2.99, 169175,        38.4, 1.179,
  "8F", 7.69,  9.53, 26.14,       74.2,  67.7,  4.5,  1.3, 272332,        58.5, 1.072,
  "8G", 3.07,  9.31, 24.19,       69.9,    42, 1.99, 0.74, 269519,        44.3, 1.152,
  "8H",  3.7,  9.14, 22.65,       71.3,  37.1, 2.07, 0.68, 272096,          40, 1.127,
  "9A", 2.58, 10.06, 24.95,       95.2, 108.4, 4.62, 3.98, 279113,        38.9, 1.082,
  "9B", 2.09,  9.95, 24.01,       95.9,  92.8, 4.06, 3.68, 279100,          50, 1.081,
  "9C", 2.18,  9.97,  24.4,      100.6, 102.7, 5.47, 4.11, 278137,        53.8, 1.078,
  "9D", 2.16,  8.96,  24.3,         42,    53, 3.19,  2.1, 174271,        50.3, 1.161,
  "9E",  1.7,  9.02, 24.72,       36.1,  63.4, 3.97, 2.55, 159046,        55.9,  1.69,
  "9F",  6.8,  9.51, 26.15,       74.4,  73.9,  3.3, 1.11, 271503,        51.3, 1.061,
  "9G", 1.95,  9.39,  23.9,       44.4,    42, 3.38, 0.69, 261124,        68.2, 1.147,
  "9H", 4.28,  8.85, 20.65,       71.3,  37.5, 1.18, 0.69, 271303,        34.2, 1.102,
  "10A", 2.58, 10.06, 24.95,       95.2, 108.4, 4.62, 3.98, 279113,        38.9, 1.082,
  "10B", 2.09,  9.95, 24.01,       95.9,  92.8, 4.06, 3.68, 279100,          50, 1.081,
  "10C", 2.98, 10.09, 24.36,       97.2, 106.9, 4.43, 3.34, 279099,          43, 1.077,
  "10D", 2.16,  8.96,  24.3,         42,    53, 3.19,  2.1, 174271,        50.3, 1.161,
  "10E",  1.7,  9.02, 24.72,       36.1,  63.4, 3.97, 2.55, 159046,        55.9,  1.69,
  "10F",  6.8,  9.51, 26.15,       74.4,  73.9,  3.3, 1.11, 271503,        51.3, 1.061,
  "10G", 1.95,  9.39,  23.9,       44.4,    42, 3.38, 0.69, 261124,        68.2, 1.147,
  "10H", 4.28,  8.85, 20.65,       71.3,  37.5, 1.18, 0.69, 271303,        34.2, 1.102,
  "11A", 2.66,    10, 24.92,        113, 111.9, 4.75, 3.21, 270193,        39.8, 1.081,
  "11B", 3.14,    10,    24,       96.9,   108, 4.48, 3.76, 279119,        38.5,  1.08,
  "11C", 2.18,  9.97,  24.4,      100.6, 102.7, 5.47, 4.11, 278137,        53.8, 1.078,
  "11D", 8.17,  9.04, 24.88,       46.9,  90.4, 2.81, 2.25, 246979,          34, 1.154,
  "11E", 2.63,     9,  24.7,       37.2,  74.9,  4.2, 2.99, 169175,        38.4, 1.179,
  "11F", 7.69,  9.53, 26.14,       74.2,  67.7,  4.5,  1.3, 272332,        58.5, 1.072,
  "11G", 3.07,  9.31, 24.19,       69.9,    42, 1.99, 0.74, 269519,        44.3, 1.152,
  "11H",  3.7,  9.14, 22.65,       71.3,  37.1, 2.07, 0.68, 272096,          40, 1.127,
  "12A", 2.66,    10, 24.92,        113, 111.9, 4.75, 3.21, 270193,        39.8, 1.081,
  "12B", 3.14,    10,    24,       96.9, 111.9, 4.48, 3.76, 279119,        38.5,  1.08,
  "12C", 2.92,  9.06, 26.46,       39.7,  23.7, 7.64, 3.66,  66608,        45.1, 1.138,
  "12D", 2.16,  8.96,  24.3,         42,    53, 3.19,  2.1, 174271,        50.3, 1.161,
  "12E",  1.7,  9.02, 24.72,       36.1,  63.4, 3.97, 2.55, 159046,        55.9,  1.69,
  "12F",  6.8,  9.51, 26.15,       74.4,  73.9,  3.3, 1.11, 271503,        51.3, 1.061,
  "12G", 1.95,  9.39,  23.9,       44.4,    42, 3.38, 0.69, 261124,        68.2, 1.147,
  "12H", 4.28,  8.85, 20.65,       71.3,  37.5, 1.18, 0.69, 271303,        34.2, 1.102
)
)

bacteria <- data.frame (tibble::tribble(
  ~index, ~Cylindrospermopsis, ~Un.Nostocaceae, ~Planktothrix, ~Un.Nostocales, ~Phormidesmis, ~Un.Cyanobiaceae, ~Un.Oxyphotobacteria, ~Un.Cyanobacteria,
  "1A",                   0,               0,             0,             12,            66,                0,                 7137,              1467,
  "1B",                   0,               0,             0,              6,            35,                0,                 5549,               238,
  "1C",                   0,              19,             2,              0,            96,                0,                 1861,               708,
  "1D",                   0,               0,             0,              0,            66,               19,                 3185,              4001,
  "1E",                   0,            1662,             0,            207,           720,              529,                 7468,              1928,
  "1F",                   0,            2090,             0,            425,           432,                6,                18421,              4460,
  "1G",                   0,             372,             0,              0,            19,                2,                 4191,               361,
  "1H",                   0,             433,           613,             46,          1215,                0,                12240,              1970,
  "2A",                   0,            1000,             0,              8,           195,                0,                20728,              4350,
  "2B",                   0,             769,            35,             62,            46,              619,                13438,              3076,
  "2C",                   0,             639,             0,             31,            14,               21,                17664,              2008,
  "2D",                   0,             510,             0,              0,            58,                0,                 5085,              2745,
  "2E",                   0,             319,             0,              0,            60,              200,                 8376,              1613,
  "2F",                   0,             501,             2,             89,           807,                0,                 8906,               983,
  "2G",                   0,             930,             0,            115,           141,              195,                13273,              1514,
  "2H",                   9,            1867,            18,            535,           279,               26,                18506,              3531,
  "3A",                  44,             272,            88,              3,          1139,                0,                 7959,              1700,
  "3B",                 570,              43,            60,             22,            65,                3,                  762,               367,
  "3C",                   0,               0,             0,              0,           173,                0,                 3088,                45,
  "3D",                   0,               0,             0,              0,             0,               52,                 3009,              1683,
  "3E",                   0,            1039,             0,            199,            74,                0,                 4120,               754,
  "3F",                   0,             388,             0,             10,           318,                0,                 5083,               675,
  "3G",                   0,             982,             0,            298,           407,                0,                 5573,              1031,
  "4A",                   0,            3272,             0,            578,           558,               32,                24267,              9707,
  "4B",                   0,             895,             0,             60,            33,             1685,                16403,              3105,
  "4C",                   0,             243,             0,              0,             0,               57,                 6043,               570,
  "4D",                   0,            1621,             0,            148,            15,                6,                 8472,              2357,
  "4E",                   0,            1094,             0,            168,           165,                0,                 8351,              2424,
  "4F",                   0,              43,             0,              0,           302,                0,                  491,               570,
  "4G",                   0,             291,             0,             74,           152,              359,                13031,              3066,
  "4H",                  16,            2814,            28,            616,          1841,                0,                33094,              6509,
  "5A",                   0,               2,             0,            111,             2,               58,                11083,              4240,
  "5B",                   0,               0,             0,              0,           108,                0,                 4248,               676,
  "5D",                   0,            1006,             0,            214,           285,                0,                 8839,              1176,
  "5E",                   0,               2,            17,            120,           355,               19,                10286,               213,
  "5F",                   0,            1051,             2,            158,           583,                0,                14778,              1765,
  "5G",                   2,            1040,            28,            587,             9,              355,                 3584,              1574,
  "5H",                   0,             244,             0,             70,            55,               22,                10905,              7012,
  "6A",                  37,            1221,             0,            126,            43,              473,                22140,              5237,
  "6B",                   0,            1190,             0,             92,           140,              599,                22958,              3646,
  "6C",                   0,             266,             0,              0,            46,                0,                 5937,              1510,
  "6D",                   0,              63,             0,              7,             0,                0,                 8240,               900,
  "6E",                   0,            1016,             0,            201,           130,                0,                 6252,              1583,
  "6F",                   0,            2226,             0,            491,           190,                0,                15494,              3392,
  "6G",                   0,             206,             0,            296,             8,              205,                 9631,              5514,
  "6H",                   0,            2014,           123,            430,          3015,               74,                40839,              7004,
  "7A",                   0,             183,             0,             16,           172,               50,                 7201,              4795,
  "7B",                   0,               0,             0,              0,             0,                0,                 2146,               732,
  "7C",                   0,              27,             0,              0,             0,                0,                 3927,               450,
  "7D",                   0,             139,           128,             42,            97,               11,                26197,              1932,
  "7E",                   0,            1266,             0,            274,          1208,                0,                17161,              4310,
  "7F",                   0,             232,           274,              3,           335,               60,                14640,               293,
  "7G",                   0,            1036,             0,            210,             5,              424,                 1888,              1837,
  "7H",                   0,             102,             0,              0,             0,                0,                 2860,              2943,
  "8A",                   0,            1096,             0,             83,            56,               16,                18949,              3364,
  "8B",                   0,            2439,             0,            263,           117,               48,                30505,              6066,
  "8C",                   0,              39,            29,              0,           102,                0,                10406,               572,
  "8D",                   0,            2214,             0,            324,            97,                0,                14814,              8608,
  "8E",                   0,            1709,           102,            323,             6,                0,                 7553,              2455,
  "8F",                   0,            2633,             0,            237,           391,                0,                24075,              3692,
  "8G",                  45,            2557,           442,            610,           108,             1817,                 7788,              4399,
  "8H",                   0,            1403,            24,            251,           256,                4,                16103,              3045,
  "9A",                   0,               2,             0,             20,             6,                0,                 3794,              1919,
  "9B",                   0,               5,             0,             30,           483,                8,                 8916,              1307,
  "9C",                   0,              46,             0,              0,             0,                0,                 2817,              1041,
  "9D",                   0,            3157,             0,            706,           162,                0,                17692,              8381,
  "9E",                   0,             342,           125,             64,          1240,              380,                20302,              2008,
  "9F",                   8,            1023,             0,            257,           584,               12,                48687,              5115,
  "9G",                   0,             407,             0,             72,            75,              195,                14834,              2512,
  "9H",                3395,            2082,          2796,            357,           540,                0,                 4402,              1391,
  "10A",                   0,             654,             0,             37,           116,              120,                14300,              3054,
  "10B",                   0,             343,             0,              0,             0,               77,                15485,              1203,
  "10C",                   0,             358,             0,              0,             0,                0,                 2695,              1719,
  "10D",                   0,              38,            47,              0,            18,               37,                13401,               342,
  "10E",                   0,            2265,             0,            382,            28,               15,                 9052,              2779,
  "10F",                   0,             824,             0,            127,            76,                0,                13282,               743,
  "10G",                   0,             338,            40,              5,           281,               13,                 2492,               939,
  "10H",                   0,             151,             0,              0,            37,                0,                 2924,               700,
  "11A",                   0,              11,             0,              0,             6,             2111,                  317,              1532,
  "11B",                   0,              27,             0,              0,             0,                0,                  968,               702,
  "11C",                   0,               0,             0,              0,            62,                9,                 4148,              2733,
  "11D",                   0,            1108,             0,            211,           165,                0,                10756,              4030,
  "11E",                   0,            1105,             0,            190,           304,                0,                10605,              1595,
  "11F",                   0,               0,             0,             19,            70,               20,                 4327,               390,
  "11G",                   0,               0,             0,             16,            54,               56,                 6701,              2077,
  "11H",                   0,              88,             0,              0,            20,                0,                14377,              1305,
  "12A",                   0,             441,             0,             50,           123,              115,                29898,              2216,
  "12B",                   0,             404,             0,              0,            59,               55,                11845,              1397,
  "12C",                   0,             623,             0,              6,            57,                0,                18824,              1992,
  "12D",                  77,            3141,           145,            695,           172,              166,                 9555,              5101,
  "12E",                   0,             172,             0,              0,            67,                5,                 6934,               243,
  "12F",                   0,            2631,             0,            425,            74,               11,                16460,              2880,
  "12G",                   2,            3522,           319,            784,           672,                0,                29848,              9140,
  "12H",                 280,            1552,           216,            350,           551,               10,                33984,              7351
)
)
library(RColorBrewer)
res1 <- cor.mtest(bind_cols(bacteria[, -1],metadata[, -1]), conf.level = 0.95)

corrr::correlate(bind_cols(metadata[, -1], bacteria[, -1])) %>%
  filter(rowname %in% colnames(metadata)) %>%
  select(one_of(c("rowname", colnames(bacteria)[-1]))) %>%
  as.data.frame() %>%
  column_to_rownames("rowname") %>%
  as.matrix() %>% 
  corrplot::corrplot(is.corr = FALSE, p.mat = res1$p[9:18, 1:8], insig= "blank", sig.level = 0.05, tl.col = "black", tl.srt = 45,
                     col= brewer.pal (n=10, name= "PuOr"))
#> 
#> Correlation method: 'pearson'
#> Missing treated using: 'pairwise.complete.obs'

Created on 2019-11-05 by the reprex package (v0.3.0.9000)

1 Like

Hi @OSDIAZ. The problem was caused by the data frame that you do cor.mtest is different from the one for correlate. So, the orientation of the two table are not the same. And also you filter the table of correlation before plot the corrplot that using by the p value of the mtest. The two dimension is not match.

I suggest the following code which do filter by p value before plot.

library(tidyverse)
library(corrplot)
#> corrplot 0.84 loaded
library(corrr)

metadata <- data.frame(tibble::tribble(
  ~SampleID,  ~DO,   ~pH, ~Temp, ~Turbidity,  ~ORP, ~NH4, ~NO3,   ~BGA, ~Chlrophyll,   ~CE,
  "1A", 4.24,  9.94, 24.48,       87.3,    97, 4.46,  3.6, 279133,        36.6, 1.074,
  "1B", 2.58, 10.06, 24.95,       95.2, 108.4, 4.62, 3.98, 279113,        38.9, 1.082,
  "1C", 2.85,  9.98, 24.01,       98.8, 102.9, 4.37, 3.57, 265304,          40, 1.081,
  "1D", 3.81,  9.07, 26.67,       24.9,    94,  5.6, 3.53,  11603,          44, 1.147,
  "1E", 2.64,  8.99, 24.01,       43.1,  63.9, 3.38, 2.55, 218471,          35, 1.156,
  "1F", 4.61,  8.93,  23.5,       49.1,  64.7, 3.21, 2.28, 226658,        32.8, 1.157,
  "1G", 5.74,  9.24, 24.46,       68.6,  40.3, 1.93, 0.71, 267389,          44, 1.072,
  "1H", 3.69,  9.32, 24.65,       69.8,  48.1, 2.21,  1.2, 267144,        44.8, 1.152,
  "2A", 4.24,  9.94, 24.48,       87.3,    97, 4.46,  3.6, 279133,        36.6, 1.074,
  "2B", 2.66,    10, 24.92,        113, 111.9, 4.75, 3.21, 270193,        39.8, 1.081,
  "2C", 2.85,  9.98, 24.01,       98.8, 102.9, 4.37, 3.57, 265304,          40, 1.081,
  "2D", 3.81,  9.07, 26.67,       24.9,    94,  5.6, 3.53,  11603,          44, 1.147,
  "2E", 2.64,  8.99, 24.01,       43.1,  63.9, 3.38, 2.55, 218471,          35, 1.156,
  "2F", 4.61,  8.93,  23.5,       49.1,  64.7, 3.21, 2.28, 226658,        32.8, 1.157,
  "2G", 5.74,  9.24, 24.46,       68.6,  40.3, 1.93, 0.71, 267389,          44, 1.072,
  "2H", 3.69,  9.32, 24.65,       69.8,  48.1, 2.21,  1.2, 267144,        44.8, 1.152,
  "3A", 2.51, 10.04, 24.35,       87.7,  91.3,  4.5, 3.36, 267716,        39.6, 1.075,
  "3B", 2.66,    10, 24.92,        113, 111.9, 4.75, 3.21, 270193,        39.8, 1.081,
  "3C", 3.14,    10,    24,       96.9,   108, 4.48, 3.76, 279119,        38.5,  1.08,
  "3D", 2.92,  9.06, 26.46,       39.7,  23.7, 7.64, 3.66,  66608,        45.1, 1.138,
  "3E", 1.83,  8.99, 23.99,         49,  64.1, 3.18, 2.44, 213497,        42.2, 1.155,
  "3F", 1.82,  8.92, 23.43,       47.6,  60.4, 3.09, 2.06, 242331,        50.2, 1.157,
  "3G", 3.02,  9.18, 24.14,       66.6,  40.6, 2.19, 0.67, 267007,        43.6, 1.061,
  "4A", 2.51, 10.04, 24.35,       87.7,  91.3,  4.5, 3.36, 267716,        39.6, 1.075,
  "4B", 3.04,  9.96, 24.04,       98.5,  98.9, 3.97, 4.35, 279109,          43, 1.083,
  "4C", 2.85,  9.98, 24.01,       98.8, 102.9, 4.37, 3.57, 265304,          40, 1.081,
  "4D", 2.92,  9.06, 26.46,       39.7,  23.7, 7.64, 3.66,  66608,        45.1, 1.138,
  "4E", 1.83,  8.99, 23.99,         49,  64.1, 3.18, 2.44, 213497,        42.2, 1.155,
  "4F", 1.82,  8.92, 23.43,       47.6,  60.4, 3.09, 2.06, 242331,        50.2, 1.157,
  "4G", 3.02,  9.18, 24.14,       66.6,  40.6, 2.19, 0.67, 267007,        43.6, 1.061,
  "4H",  3.3,  9.32, 24.67,       74.1,  49.8, 2.14, 0.87, 261363,        45.1, 1.142,
  "5A", 4.24,  9.94, 24.48,       87.3,    97, 4.46,  3.6, 279133,        36.6, 1.074,
  "5B", 3.04,  9.96, 24.04,       98.5,  98.9, 3.97, 4.35, 279109,          43, 1.083,
  "5D", 3.81,  9.07, 26.67,       24.9,    94,  5.6, 3.53,  11603,          44, 1.147,
  "5E", 2.64,  8.99, 24.01,       43.1,  63.9, 3.38, 2.55, 218471,          35, 1.156,
  "5F", 4.61,  8.93,  23.5,       49.1,  64.7, 3.21, 2.28, 226658,        32.8, 1.157,
  "5G", 5.74,  9.24, 24.46,       68.6,  40.3, 1.93, 0.71, 267389,          44, 1.072,
  "5H", 3.69,  9.32, 24.65,       69.8,  48.1, 2.21,  1.2, 267144,        44.8, 1.152,
  "6A", 4.24,  9.94, 24.48,       87.3,    97, 4.46,  3.6, 279133,        36.6, 1.074,
  "6B", 2.09,  9.95, 24.01,       95.9,  92.8, 4.06, 3.68, 279100,          50, 1.077,
  "6C", 2.98, 10.09, 24.36,       97.2, 106.9, 4.43, 3.34, 279099,          43, 1.077,
  "6D", 3.81,  9.07, 26.67,       24.9,    94,  5.6, 3.53,  11603,          44, 1.147,
  "6E", 1.83,  8.99, 23.99,         49,  64.1, 3.18, 2.44, 213497,        42.2, 1.155,
  "6F", 1.82,  8.92, 23.43,       47.6,  60.4, 3.09, 2.06, 242331,        50.2, 1.157,
  "6G", 3.02,  9.18, 24.14,       66.6,  40.6, 2.19, 0.67, 267007,        43.6, 1.061,
  "6H",  3.3,  9.32, 24.67,       74.1,  49.8, 2.14, 0.87, 261363,        45.1, 1.142,
  "7A", 2.51, 10.04, 24.35,       87.7,  91.3,  4.5, 3.36, 267716,        39.6, 1.075,
  "7B", 2.09,  9.95, 24.01,       95.9,  92.8, 4.06, 3.68, 279100,          50, 1.081,
  "7C", 2.98, 10.09, 24.36,       97.2, 106.9, 4.43, 3.34, 279099,          43, 1.077,
  "7D", 8.17,  9.04, 24.88,       46.9,  90.4, 2.81, 2.25, 246979,          34, 1.154,
  "7E", 2.63,     9,  24.7,       37.2,  74.9,  4.2, 2.99, 169175,        38.4, 1.179,
  "7F", 7.69,  9.53, 26.14,       74.2,  67.7,  4.5,  1.3, 272332,        58.5, 1.072,
  "7G", 3.07,  9.31, 24.19,       69.9,    42, 1.99, 0.74, 269519,        44.3, 1.152,
  "7H",  3.7,  9.14, 22.65,       71.3,  37.1, 2.07, 0.68, 272096,          40, 1.127,
  "8A", 2.51, 10.04, 24.35,       87.7,  91.3,  4.5, 3.36, 267716,        39.6, 1.075,
  "8B", 3.04,  9.96, 24.04,       98.5,  98.9, 3.97, 4.35, 279109,          43, 1.083,
  "8C", 2.18,  9.97,  24.4,      100.6, 102.7, 5.47, 4.11, 278137,        53.8, 1.078,
  "8D", 8.17,  9.04, 24.88,       46.9,  90.4, 2.81, 2.25, 246979,          34, 1.154,
  "8E", 2.63,     9,  24.7,       37.2,  74.9,  4.2, 2.99, 169175,        38.4, 1.179,
  "8F", 7.69,  9.53, 26.14,       74.2,  67.7,  4.5,  1.3, 272332,        58.5, 1.072,
  "8G", 3.07,  9.31, 24.19,       69.9,    42, 1.99, 0.74, 269519,        44.3, 1.152,
  "8H",  3.7,  9.14, 22.65,       71.3,  37.1, 2.07, 0.68, 272096,          40, 1.127,
  "9A", 2.58, 10.06, 24.95,       95.2, 108.4, 4.62, 3.98, 279113,        38.9, 1.082,
  "9B", 2.09,  9.95, 24.01,       95.9,  92.8, 4.06, 3.68, 279100,          50, 1.081,
  "9C", 2.18,  9.97,  24.4,      100.6, 102.7, 5.47, 4.11, 278137,        53.8, 1.078,
  "9D", 2.16,  8.96,  24.3,         42,    53, 3.19,  2.1, 174271,        50.3, 1.161,
  "9E",  1.7,  9.02, 24.72,       36.1,  63.4, 3.97, 2.55, 159046,        55.9,  1.69,
  "9F",  6.8,  9.51, 26.15,       74.4,  73.9,  3.3, 1.11, 271503,        51.3, 1.061,
  "9G", 1.95,  9.39,  23.9,       44.4,    42, 3.38, 0.69, 261124,        68.2, 1.147,
  "9H", 4.28,  8.85, 20.65,       71.3,  37.5, 1.18, 0.69, 271303,        34.2, 1.102,
  "10A", 2.58, 10.06, 24.95,       95.2, 108.4, 4.62, 3.98, 279113,        38.9, 1.082,
  "10B", 2.09,  9.95, 24.01,       95.9,  92.8, 4.06, 3.68, 279100,          50, 1.081,
  "10C", 2.98, 10.09, 24.36,       97.2, 106.9, 4.43, 3.34, 279099,          43, 1.077,
  "10D", 2.16,  8.96,  24.3,         42,    53, 3.19,  2.1, 174271,        50.3, 1.161,
  "10E",  1.7,  9.02, 24.72,       36.1,  63.4, 3.97, 2.55, 159046,        55.9,  1.69,
  "10F",  6.8,  9.51, 26.15,       74.4,  73.9,  3.3, 1.11, 271503,        51.3, 1.061,
  "10G", 1.95,  9.39,  23.9,       44.4,    42, 3.38, 0.69, 261124,        68.2, 1.147,
  "10H", 4.28,  8.85, 20.65,       71.3,  37.5, 1.18, 0.69, 271303,        34.2, 1.102,
  "11A", 2.66,    10, 24.92,        113, 111.9, 4.75, 3.21, 270193,        39.8, 1.081,
  "11B", 3.14,    10,    24,       96.9,   108, 4.48, 3.76, 279119,        38.5,  1.08,
  "11C", 2.18,  9.97,  24.4,      100.6, 102.7, 5.47, 4.11, 278137,        53.8, 1.078,
  "11D", 8.17,  9.04, 24.88,       46.9,  90.4, 2.81, 2.25, 246979,          34, 1.154,
  "11E", 2.63,     9,  24.7,       37.2,  74.9,  4.2, 2.99, 169175,        38.4, 1.179,
  "11F", 7.69,  9.53, 26.14,       74.2,  67.7,  4.5,  1.3, 272332,        58.5, 1.072,
  "11G", 3.07,  9.31, 24.19,       69.9,    42, 1.99, 0.74, 269519,        44.3, 1.152,
  "11H",  3.7,  9.14, 22.65,       71.3,  37.1, 2.07, 0.68, 272096,          40, 1.127,
  "12A", 2.66,    10, 24.92,        113, 111.9, 4.75, 3.21, 270193,        39.8, 1.081,
  "12B", 3.14,    10,    24,       96.9, 111.9, 4.48, 3.76, 279119,        38.5,  1.08,
  "12C", 2.92,  9.06, 26.46,       39.7,  23.7, 7.64, 3.66,  66608,        45.1, 1.138,
  "12D", 2.16,  8.96,  24.3,         42,    53, 3.19,  2.1, 174271,        50.3, 1.161,
  "12E",  1.7,  9.02, 24.72,       36.1,  63.4, 3.97, 2.55, 159046,        55.9,  1.69,
  "12F",  6.8,  9.51, 26.15,       74.4,  73.9,  3.3, 1.11, 271503,        51.3, 1.061,
  "12G", 1.95,  9.39,  23.9,       44.4,    42, 3.38, 0.69, 261124,        68.2, 1.147,
  "12H", 4.28,  8.85, 20.65,       71.3,  37.5, 1.18, 0.69, 271303,        34.2, 1.102
)
)

bacteria <- data.frame (tibble::tribble(
  ~index, ~Cylindrospermopsis, ~Un.Nostocaceae, ~Planktothrix, ~Un.Nostocales, ~Phormidesmis, ~Un.Cyanobiaceae, ~Un.Oxyphotobacteria, ~Un.Cyanobacteria,
  "1A",                   0,               0,             0,             12,            66,                0,                 7137,              1467,
  "1B",                   0,               0,             0,              6,            35,                0,                 5549,               238,
  "1C",                   0,              19,             2,              0,            96,                0,                 1861,               708,
  "1D",                   0,               0,             0,              0,            66,               19,                 3185,              4001,
  "1E",                   0,            1662,             0,            207,           720,              529,                 7468,              1928,
  "1F",                   0,            2090,             0,            425,           432,                6,                18421,              4460,
  "1G",                   0,             372,             0,              0,            19,                2,                 4191,               361,
  "1H",                   0,             433,           613,             46,          1215,                0,                12240,              1970,
  "2A",                   0,            1000,             0,              8,           195,                0,                20728,              4350,
  "2B",                   0,             769,            35,             62,            46,              619,                13438,              3076,
  "2C",                   0,             639,             0,             31,            14,               21,                17664,              2008,
  "2D",                   0,             510,             0,              0,            58,                0,                 5085,              2745,
  "2E",                   0,             319,             0,              0,            60,              200,                 8376,              1613,
  "2F",                   0,             501,             2,             89,           807,                0,                 8906,               983,
  "2G",                   0,             930,             0,            115,           141,              195,                13273,              1514,
  "2H",                   9,            1867,            18,            535,           279,               26,                18506,              3531,
  "3A",                  44,             272,            88,              3,          1139,                0,                 7959,              1700,
  "3B",                 570,              43,            60,             22,            65,                3,                  762,               367,
  "3C",                   0,               0,             0,              0,           173,                0,                 3088,                45,
  "3D",                   0,               0,             0,              0,             0,               52,                 3009,              1683,
  "3E",                   0,            1039,             0,            199,            74,                0,                 4120,               754,
  "3F",                   0,             388,             0,             10,           318,                0,                 5083,               675,
  "3G",                   0,             982,             0,            298,           407,                0,                 5573,              1031,
  "4A",                   0,            3272,             0,            578,           558,               32,                24267,              9707,
  "4B",                   0,             895,             0,             60,            33,             1685,                16403,              3105,
  "4C",                   0,             243,             0,              0,             0,               57,                 6043,               570,
  "4D",                   0,            1621,             0,            148,            15,                6,                 8472,              2357,
  "4E",                   0,            1094,             0,            168,           165,                0,                 8351,              2424,
  "4F",                   0,              43,             0,              0,           302,                0,                  491,               570,
  "4G",                   0,             291,             0,             74,           152,              359,                13031,              3066,
  "4H",                  16,            2814,            28,            616,          1841,                0,                33094,              6509,
  "5A",                   0,               2,             0,            111,             2,               58,                11083,              4240,
  "5B",                   0,               0,             0,              0,           108,                0,                 4248,               676,
  "5D",                   0,            1006,             0,            214,           285,                0,                 8839,              1176,
  "5E",                   0,               2,            17,            120,           355,               19,                10286,               213,
  "5F",                   0,            1051,             2,            158,           583,                0,                14778,              1765,
  "5G",                   2,            1040,            28,            587,             9,              355,                 3584,              1574,
  "5H",                   0,             244,             0,             70,            55,               22,                10905,              7012,
  "6A",                  37,            1221,             0,            126,            43,              473,                22140,              5237,
  "6B",                   0,            1190,             0,             92,           140,              599,                22958,              3646,
  "6C",                   0,             266,             0,              0,            46,                0,                 5937,              1510,
  "6D",                   0,              63,             0,              7,             0,                0,                 8240,               900,
  "6E",                   0,            1016,             0,            201,           130,                0,                 6252,              1583,
  "6F",                   0,            2226,             0,            491,           190,                0,                15494,              3392,
  "6G",                   0,             206,             0,            296,             8,              205,                 9631,              5514,
  "6H",                   0,            2014,           123,            430,          3015,               74,                40839,              7004,
  "7A",                   0,             183,             0,             16,           172,               50,                 7201,              4795,
  "7B",                   0,               0,             0,              0,             0,                0,                 2146,               732,
  "7C",                   0,              27,             0,              0,             0,                0,                 3927,               450,
  "7D",                   0,             139,           128,             42,            97,               11,                26197,              1932,
  "7E",                   0,            1266,             0,            274,          1208,                0,                17161,              4310,
  "7F",                   0,             232,           274,              3,           335,               60,                14640,               293,
  "7G",                   0,            1036,             0,            210,             5,              424,                 1888,              1837,
  "7H",                   0,             102,             0,              0,             0,                0,                 2860,              2943,
  "8A",                   0,            1096,             0,             83,            56,               16,                18949,              3364,
  "8B",                   0,            2439,             0,            263,           117,               48,                30505,              6066,
  "8C",                   0,              39,            29,              0,           102,                0,                10406,               572,
  "8D",                   0,            2214,             0,            324,            97,                0,                14814,              8608,
  "8E",                   0,            1709,           102,            323,             6,                0,                 7553,              2455,
  "8F",                   0,            2633,             0,            237,           391,                0,                24075,              3692,
  "8G",                  45,            2557,           442,            610,           108,             1817,                 7788,              4399,
  "8H",                   0,            1403,            24,            251,           256,                4,                16103,              3045,
  "9A",                   0,               2,             0,             20,             6,                0,                 3794,              1919,
  "9B",                   0,               5,             0,             30,           483,                8,                 8916,              1307,
  "9C",                   0,              46,             0,              0,             0,                0,                 2817,              1041,
  "9D",                   0,            3157,             0,            706,           162,                0,                17692,              8381,
  "9E",                   0,             342,           125,             64,          1240,              380,                20302,              2008,
  "9F",                   8,            1023,             0,            257,           584,               12,                48687,              5115,
  "9G",                   0,             407,             0,             72,            75,              195,                14834,              2512,
  "9H",                3395,            2082,          2796,            357,           540,                0,                 4402,              1391,
  "10A",                   0,             654,             0,             37,           116,              120,                14300,              3054,
  "10B",                   0,             343,             0,              0,             0,               77,                15485,              1203,
  "10C",                   0,             358,             0,              0,             0,                0,                 2695,              1719,
  "10D",                   0,              38,            47,              0,            18,               37,                13401,               342,
  "10E",                   0,            2265,             0,            382,            28,               15,                 9052,              2779,
  "10F",                   0,             824,             0,            127,            76,                0,                13282,               743,
  "10G",                   0,             338,            40,              5,           281,               13,                 2492,               939,
  "10H",                   0,             151,             0,              0,            37,                0,                 2924,               700,
  "11A",                   0,              11,             0,              0,             6,             2111,                  317,              1532,
  "11B",                   0,              27,             0,              0,             0,                0,                  968,               702,
  "11C",                   0,               0,             0,              0,            62,                9,                 4148,              2733,
  "11D",                   0,            1108,             0,            211,           165,                0,                10756,              4030,
  "11E",                   0,            1105,             0,            190,           304,                0,                10605,              1595,
  "11F",                   0,               0,             0,             19,            70,               20,                 4327,               390,
  "11G",                   0,               0,             0,             16,            54,               56,                 6701,              2077,
  "11H",                   0,              88,             0,              0,            20,                0,                14377,              1305,
  "12A",                   0,             441,             0,             50,           123,              115,                29898,              2216,
  "12B",                   0,             404,             0,              0,            59,               55,                11845,              1397,
  "12C",                   0,             623,             0,              6,            57,                0,                18824,              1992,
  "12D",                  77,            3141,           145,            695,           172,              166,                 9555,              5101,
  "12E",                   0,             172,             0,              0,            67,                5,                 6934,               243,
  "12F",                   0,            2631,             0,            425,            74,               11,                16460,              2880,
  "12G",                   2,            3522,           319,            784,           672,                0,                29848,              9140,
  "12H",                 280,            1552,           216,            350,           551,               10,                33984,              7351
)
)
library(RColorBrewer)
df <- bind_cols(bacteria[, -1],metadata[, -1])

res1 <- cor.mtest(df, conf.level = 0.95)
res2 <- res1$p %>%
  as.data.frame() %>%
  `rownames<-`(colnames(df)) %>%
  `colnames<-`(colnames(df)) %>%
  rownames_to_column("rowname") %>%
  gather("var", "p", -rowname)

corrr::correlate(bind_cols(metadata[, -1], bacteria[, -1])) %>%
  gather("var", "value", -rowname) %>%
  left_join(res2) %>%
  mutate(value = ifelse(p < 0.05, NA_integer_, value)) %>%
  select(-p) %>%
  spread(var, value) %>%
  filter(rowname %in% colnames(metadata)) %>%
  select(one_of(c("rowname", colnames(bacteria)[-1]))) %>%
  as.data.frame() %>%
  column_to_rownames("rowname") %>%
  as.matrix() %>%
  corrplot::corrplot(is.corr = FALSE, na.label.col = "white", col = brewer.pal (n=10, name= "PuOr"), tl.col = "black", tl.srt = 45)
#> 
#> Correlation method: 'pearson'
#> Missing treated using: 'pairwise.complete.obs'
#> Joining, by = c("rowname", "var")

Created on 2019-11-06 by the reprex package (v0.3.0)

1 Like

Thank you very much for helping me, although I still think that the analysis is not correct.

The reason I think the statistical analysis is not correct is because almost the entire NH4 row was removed when the initial circles had a very high correlation with the bacteria. I don't think the p-value for this variable is less than 0.05. The circles that I believe should be eliminated according to what I have observed in scientific articles (less than 0.05) are the smallest as BGA-Un. Nostocales, CE-Un. Oxyphotobacteria.

However, I thank you very much for your help, I appreciate it very much.

This is the original correlation matrix without the removal of those with a lower level of significance

Thank you very much for your help I really aprecciate it, I made a comment below with the doubts that continue to be generated according to this analysis.

@OSDIAZ - I think your terminology is causing some confusion. For example, you say

The reason I think the statistical analysis is not correct is because almost the entire NH4 row was removed when the initial circles had a very high correlation with the bacteria. I don't think the p-value for this variable is less than 0.05.

The high correlation in the NH4 row would be expected to result in low p values, i.e. more likely to be judged a significant effect. Because you asked in your first post that groups with p < 0.05 be eliminated, that is what @raytong did. Note this line in raytong's code:

mutate(value = ifelse(p < 0.05, NA_integer_, value))

My code keeps the correlations with p <= 0.05 and so produces the inverse of raytong's graph. You can check the p value of any combination of variables manually. Note below that the p value of Un.Nostocales with NH4 is small but with BGA it is high.

metadata <- data.frame(tibble::tribble(
  ~SampleID,  ~DO,   ~pH, ~Temp, ~Turbidity,  ~ORP, ~NH4, ~NO3,   ~BGA, ~Chlrophyll,   ~CE,
  "1A", 4.24,  9.94, 24.48,       87.3,    97, 4.46,  3.6, 279133,        36.6, 1.074,
  "1B", 2.58, 10.06, 24.95,       95.2, 108.4, 4.62, 3.98, 279113,        38.9, 1.082,
  "1C", 2.85,  9.98, 24.01,       98.8, 102.9, 4.37, 3.57, 265304,          40, 1.081,
  "1D", 3.81,  9.07, 26.67,       24.9,    94,  5.6, 3.53,  11603,          44, 1.147,
  "1E", 2.64,  8.99, 24.01,       43.1,  63.9, 3.38, 2.55, 218471,          35, 1.156,
  "1F", 4.61,  8.93,  23.5,       49.1,  64.7, 3.21, 2.28, 226658,        32.8, 1.157,
  "1G", 5.74,  9.24, 24.46,       68.6,  40.3, 1.93, 0.71, 267389,          44, 1.072,
  "1H", 3.69,  9.32, 24.65,       69.8,  48.1, 2.21,  1.2, 267144,        44.8, 1.152,
  "2A", 4.24,  9.94, 24.48,       87.3,    97, 4.46,  3.6, 279133,        36.6, 1.074,
  "2B", 2.66,    10, 24.92,        113, 111.9, 4.75, 3.21, 270193,        39.8, 1.081,
  "2C", 2.85,  9.98, 24.01,       98.8, 102.9, 4.37, 3.57, 265304,          40, 1.081,
  "2D", 3.81,  9.07, 26.67,       24.9,    94,  5.6, 3.53,  11603,          44, 1.147,
  "2E", 2.64,  8.99, 24.01,       43.1,  63.9, 3.38, 2.55, 218471,          35, 1.156,
  "2F", 4.61,  8.93,  23.5,       49.1,  64.7, 3.21, 2.28, 226658,        32.8, 1.157,
  "2G", 5.74,  9.24, 24.46,       68.6,  40.3, 1.93, 0.71, 267389,          44, 1.072,
  "2H", 3.69,  9.32, 24.65,       69.8,  48.1, 2.21,  1.2, 267144,        44.8, 1.152,
  "3A", 2.51, 10.04, 24.35,       87.7,  91.3,  4.5, 3.36, 267716,        39.6, 1.075,
  "3B", 2.66,    10, 24.92,        113, 111.9, 4.75, 3.21, 270193,        39.8, 1.081,
  "3C", 3.14,    10,    24,       96.9,   108, 4.48, 3.76, 279119,        38.5,  1.08,
  "3D", 2.92,  9.06, 26.46,       39.7,  23.7, 7.64, 3.66,  66608,        45.1, 1.138,
  "3E", 1.83,  8.99, 23.99,         49,  64.1, 3.18, 2.44, 213497,        42.2, 1.155,
  "3F", 1.82,  8.92, 23.43,       47.6,  60.4, 3.09, 2.06, 242331,        50.2, 1.157,
  "3G", 3.02,  9.18, 24.14,       66.6,  40.6, 2.19, 0.67, 267007,        43.6, 1.061,
  "4A", 2.51, 10.04, 24.35,       87.7,  91.3,  4.5, 3.36, 267716,        39.6, 1.075,
  "4B", 3.04,  9.96, 24.04,       98.5,  98.9, 3.97, 4.35, 279109,          43, 1.083,
  "4C", 2.85,  9.98, 24.01,       98.8, 102.9, 4.37, 3.57, 265304,          40, 1.081,
  "4D", 2.92,  9.06, 26.46,       39.7,  23.7, 7.64, 3.66,  66608,        45.1, 1.138,
  "4E", 1.83,  8.99, 23.99,         49,  64.1, 3.18, 2.44, 213497,        42.2, 1.155,
  "4F", 1.82,  8.92, 23.43,       47.6,  60.4, 3.09, 2.06, 242331,        50.2, 1.157,
  "4G", 3.02,  9.18, 24.14,       66.6,  40.6, 2.19, 0.67, 267007,        43.6, 1.061,
  "4H",  3.3,  9.32, 24.67,       74.1,  49.8, 2.14, 0.87, 261363,        45.1, 1.142,
  "5A", 4.24,  9.94, 24.48,       87.3,    97, 4.46,  3.6, 279133,        36.6, 1.074,
  "5B", 3.04,  9.96, 24.04,       98.5,  98.9, 3.97, 4.35, 279109,          43, 1.083,
  "5D", 3.81,  9.07, 26.67,       24.9,    94,  5.6, 3.53,  11603,          44, 1.147,
  "5E", 2.64,  8.99, 24.01,       43.1,  63.9, 3.38, 2.55, 218471,          35, 1.156,
  "5F", 4.61,  8.93,  23.5,       49.1,  64.7, 3.21, 2.28, 226658,        32.8, 1.157,
  "5G", 5.74,  9.24, 24.46,       68.6,  40.3, 1.93, 0.71, 267389,          44, 1.072,
  "5H", 3.69,  9.32, 24.65,       69.8,  48.1, 2.21,  1.2, 267144,        44.8, 1.152,
  "6A", 4.24,  9.94, 24.48,       87.3,    97, 4.46,  3.6, 279133,        36.6, 1.074,
  "6B", 2.09,  9.95, 24.01,       95.9,  92.8, 4.06, 3.68, 279100,          50, 1.077,
  "6C", 2.98, 10.09, 24.36,       97.2, 106.9, 4.43, 3.34, 279099,          43, 1.077,
  "6D", 3.81,  9.07, 26.67,       24.9,    94,  5.6, 3.53,  11603,          44, 1.147,
  "6E", 1.83,  8.99, 23.99,         49,  64.1, 3.18, 2.44, 213497,        42.2, 1.155,
  "6F", 1.82,  8.92, 23.43,       47.6,  60.4, 3.09, 2.06, 242331,        50.2, 1.157,
  "6G", 3.02,  9.18, 24.14,       66.6,  40.6, 2.19, 0.67, 267007,        43.6, 1.061,
  "6H",  3.3,  9.32, 24.67,       74.1,  49.8, 2.14, 0.87, 261363,        45.1, 1.142,
  "7A", 2.51, 10.04, 24.35,       87.7,  91.3,  4.5, 3.36, 267716,        39.6, 1.075,
  "7B", 2.09,  9.95, 24.01,       95.9,  92.8, 4.06, 3.68, 279100,          50, 1.081,
  "7C", 2.98, 10.09, 24.36,       97.2, 106.9, 4.43, 3.34, 279099,          43, 1.077,
  "7D", 8.17,  9.04, 24.88,       46.9,  90.4, 2.81, 2.25, 246979,          34, 1.154,
  "7E", 2.63,     9,  24.7,       37.2,  74.9,  4.2, 2.99, 169175,        38.4, 1.179,
  "7F", 7.69,  9.53, 26.14,       74.2,  67.7,  4.5,  1.3, 272332,        58.5, 1.072,
  "7G", 3.07,  9.31, 24.19,       69.9,    42, 1.99, 0.74, 269519,        44.3, 1.152,
  "7H",  3.7,  9.14, 22.65,       71.3,  37.1, 2.07, 0.68, 272096,          40, 1.127,
  "8A", 2.51, 10.04, 24.35,       87.7,  91.3,  4.5, 3.36, 267716,        39.6, 1.075,
  "8B", 3.04,  9.96, 24.04,       98.5,  98.9, 3.97, 4.35, 279109,          43, 1.083,
  "8C", 2.18,  9.97,  24.4,      100.6, 102.7, 5.47, 4.11, 278137,        53.8, 1.078,
  "8D", 8.17,  9.04, 24.88,       46.9,  90.4, 2.81, 2.25, 246979,          34, 1.154,
  "8E", 2.63,     9,  24.7,       37.2,  74.9,  4.2, 2.99, 169175,        38.4, 1.179,
  "8F", 7.69,  9.53, 26.14,       74.2,  67.7,  4.5,  1.3, 272332,        58.5, 1.072,
  "8G", 3.07,  9.31, 24.19,       69.9,    42, 1.99, 0.74, 269519,        44.3, 1.152,
  "8H",  3.7,  9.14, 22.65,       71.3,  37.1, 2.07, 0.68, 272096,          40, 1.127,
  "9A", 2.58, 10.06, 24.95,       95.2, 108.4, 4.62, 3.98, 279113,        38.9, 1.082,
  "9B", 2.09,  9.95, 24.01,       95.9,  92.8, 4.06, 3.68, 279100,          50, 1.081,
  "9C", 2.18,  9.97,  24.4,      100.6, 102.7, 5.47, 4.11, 278137,        53.8, 1.078,
  "9D", 2.16,  8.96,  24.3,         42,    53, 3.19,  2.1, 174271,        50.3, 1.161,
  "9E",  1.7,  9.02, 24.72,       36.1,  63.4, 3.97, 2.55, 159046,        55.9,  1.69,
  "9F",  6.8,  9.51, 26.15,       74.4,  73.9,  3.3, 1.11, 271503,        51.3, 1.061,
  "9G", 1.95,  9.39,  23.9,       44.4,    42, 3.38, 0.69, 261124,        68.2, 1.147,
  "9H", 4.28,  8.85, 20.65,       71.3,  37.5, 1.18, 0.69, 271303,        34.2, 1.102,
  "10A", 2.58, 10.06, 24.95,       95.2, 108.4, 4.62, 3.98, 279113,        38.9, 1.082,
  "10B", 2.09,  9.95, 24.01,       95.9,  92.8, 4.06, 3.68, 279100,          50, 1.081,
  "10C", 2.98, 10.09, 24.36,       97.2, 106.9, 4.43, 3.34, 279099,          43, 1.077,
  "10D", 2.16,  8.96,  24.3,         42,    53, 3.19,  2.1, 174271,        50.3, 1.161,
  "10E",  1.7,  9.02, 24.72,       36.1,  63.4, 3.97, 2.55, 159046,        55.9,  1.69,
  "10F",  6.8,  9.51, 26.15,       74.4,  73.9,  3.3, 1.11, 271503,        51.3, 1.061,
  "10G", 1.95,  9.39,  23.9,       44.4,    42, 3.38, 0.69, 261124,        68.2, 1.147,
  "10H", 4.28,  8.85, 20.65,       71.3,  37.5, 1.18, 0.69, 271303,        34.2, 1.102,
  "11A", 2.66,    10, 24.92,        113, 111.9, 4.75, 3.21, 270193,        39.8, 1.081,
  "11B", 3.14,    10,    24,       96.9,   108, 4.48, 3.76, 279119,        38.5,  1.08,
  "11C", 2.18,  9.97,  24.4,      100.6, 102.7, 5.47, 4.11, 278137,        53.8, 1.078,
  "11D", 8.17,  9.04, 24.88,       46.9,  90.4, 2.81, 2.25, 246979,          34, 1.154,
  "11E", 2.63,     9,  24.7,       37.2,  74.9,  4.2, 2.99, 169175,        38.4, 1.179,
  "11F", 7.69,  9.53, 26.14,       74.2,  67.7,  4.5,  1.3, 272332,        58.5, 1.072,
  "11G", 3.07,  9.31, 24.19,       69.9,    42, 1.99, 0.74, 269519,        44.3, 1.152,
  "11H",  3.7,  9.14, 22.65,       71.3,  37.1, 2.07, 0.68, 272096,          40, 1.127,
  "12A", 2.66,    10, 24.92,        113, 111.9, 4.75, 3.21, 270193,        39.8, 1.081,
  "12B", 3.14,    10,    24,       96.9, 111.9, 4.48, 3.76, 279119,        38.5,  1.08,
  "12C", 2.92,  9.06, 26.46,       39.7,  23.7, 7.64, 3.66,  66608,        45.1, 1.138,
  "12D", 2.16,  8.96,  24.3,         42,    53, 3.19,  2.1, 174271,        50.3, 1.161,
  "12E",  1.7,  9.02, 24.72,       36.1,  63.4, 3.97, 2.55, 159046,        55.9,  1.69,
  "12F",  6.8,  9.51, 26.15,       74.4,  73.9,  3.3, 1.11, 271503,        51.3, 1.061,
  "12G", 1.95,  9.39,  23.9,       44.4,    42, 3.38, 0.69, 261124,        68.2, 1.147,
  "12H", 4.28,  8.85, 20.65,       71.3,  37.5, 1.18, 0.69, 271303,        34.2, 1.102
)
)

bacteria <- data.frame (tibble::tribble(
  ~index, ~Cylindrospermopsis, ~Un.Nostocaceae, ~Planktothrix, ~Un.Nostocales, ~Phormidesmis, ~Un.Cyanobiaceae, ~Un.Oxyphotobacteria, ~Un.Cyanobacteria,
  "1A",                   0,               0,             0,             12,            66,                0,                 7137,              1467,
  "1B",                   0,               0,             0,              6,            35,                0,                 5549,               238,
  "1C",                   0,              19,             2,              0,            96,                0,                 1861,               708,
  "1D",                   0,               0,             0,              0,            66,               19,                 3185,              4001,
  "1E",                   0,            1662,             0,            207,           720,              529,                 7468,              1928,
  "1F",                   0,            2090,             0,            425,           432,                6,                18421,              4460,
  "1G",                   0,             372,             0,              0,            19,                2,                 4191,               361,
  "1H",                   0,             433,           613,             46,          1215,                0,                12240,              1970,
  "2A",                   0,            1000,             0,              8,           195,                0,                20728,              4350,
  "2B",                   0,             769,            35,             62,            46,              619,                13438,              3076,
  "2C",                   0,             639,             0,             31,            14,               21,                17664,              2008,
  "2D",                   0,             510,             0,              0,            58,                0,                 5085,              2745,
  "2E",                   0,             319,             0,              0,            60,              200,                 8376,              1613,
  "2F",                   0,             501,             2,             89,           807,                0,                 8906,               983,
  "2G",                   0,             930,             0,            115,           141,              195,                13273,              1514,
  "2H",                   9,            1867,            18,            535,           279,               26,                18506,              3531,
  "3A",                  44,             272,            88,              3,          1139,                0,                 7959,              1700,
  "3B",                 570,              43,            60,             22,            65,                3,                  762,               367,
  "3C",                   0,               0,             0,              0,           173,                0,                 3088,                45,
  "3D",                   0,               0,             0,              0,             0,               52,                 3009,              1683,
  "3E",                   0,            1039,             0,            199,            74,                0,                 4120,               754,
  "3F",                   0,             388,             0,             10,           318,                0,                 5083,               675,
  "3G",                   0,             982,             0,            298,           407,                0,                 5573,              1031,
  "4A",                   0,            3272,             0,            578,           558,               32,                24267,              9707,
  "4B",                   0,             895,             0,             60,            33,             1685,                16403,              3105,
  "4C",                   0,             243,             0,              0,             0,               57,                 6043,               570,
  "4D",                   0,            1621,             0,            148,            15,                6,                 8472,              2357,
  "4E",                   0,            1094,             0,            168,           165,                0,                 8351,              2424,
  "4F",                   0,              43,             0,              0,           302,                0,                  491,               570,
  "4G",                   0,             291,             0,             74,           152,              359,                13031,              3066,
  "4H",                  16,            2814,            28,            616,          1841,                0,                33094,              6509,
  "5A",                   0,               2,             0,            111,             2,               58,                11083,              4240,
  "5B",                   0,               0,             0,              0,           108,                0,                 4248,               676,
  "5D",                   0,            1006,             0,            214,           285,                0,                 8839,              1176,
  "5E",                   0,               2,            17,            120,           355,               19,                10286,               213,
  "5F",                   0,            1051,             2,            158,           583,                0,                14778,              1765,
  "5G",                   2,            1040,            28,            587,             9,              355,                 3584,              1574,
  "5H",                   0,             244,             0,             70,            55,               22,                10905,              7012,
  "6A",                  37,            1221,             0,            126,            43,              473,                22140,              5237,
  "6B",                   0,            1190,             0,             92,           140,              599,                22958,              3646,
  "6C",                   0,             266,             0,              0,            46,                0,                 5937,              1510,
  "6D",                   0,              63,             0,              7,             0,                0,                 8240,               900,
  "6E",                   0,            1016,             0,            201,           130,                0,                 6252,              1583,
  "6F",                   0,            2226,             0,            491,           190,                0,                15494,              3392,
  "6G",                   0,             206,             0,            296,             8,              205,                 9631,              5514,
  "6H",                   0,            2014,           123,            430,          3015,               74,                40839,              7004,
  "7A",                   0,             183,             0,             16,           172,               50,                 7201,              4795,
  "7B",                   0,               0,             0,              0,             0,                0,                 2146,               732,
  "7C",                   0,              27,             0,              0,             0,                0,                 3927,               450,
  "7D",                   0,             139,           128,             42,            97,               11,                26197,              1932,
  "7E",                   0,            1266,             0,            274,          1208,                0,                17161,              4310,
  "7F",                   0,             232,           274,              3,           335,               60,                14640,               293,
  "7G",                   0,            1036,             0,            210,             5,              424,                 1888,              1837,
  "7H",                   0,             102,             0,              0,             0,                0,                 2860,              2943,
  "8A",                   0,            1096,             0,             83,            56,               16,                18949,              3364,
  "8B",                   0,            2439,             0,            263,           117,               48,                30505,              6066,
  "8C",                   0,              39,            29,              0,           102,                0,                10406,               572,
  "8D",                   0,            2214,             0,            324,            97,                0,                14814,              8608,
  "8E",                   0,            1709,           102,            323,             6,                0,                 7553,              2455,
  "8F",                   0,            2633,             0,            237,           391,                0,                24075,              3692,
  "8G",                  45,            2557,           442,            610,           108,             1817,                 7788,              4399,
  "8H",                   0,            1403,            24,            251,           256,                4,                16103,              3045,
  "9A",                   0,               2,             0,             20,             6,                0,                 3794,              1919,
  "9B",                   0,               5,             0,             30,           483,                8,                 8916,              1307,
  "9C",                   0,              46,             0,              0,             0,                0,                 2817,              1041,
  "9D",                   0,            3157,             0,            706,           162,                0,                17692,              8381,
  "9E",                   0,             342,           125,             64,          1240,              380,                20302,              2008,
  "9F",                   8,            1023,             0,            257,           584,               12,                48687,              5115,
  "9G",                   0,             407,             0,             72,            75,              195,                14834,              2512,
  "9H",                3395,            2082,          2796,            357,           540,                0,                 4402,              1391,
  "10A",                   0,             654,             0,             37,           116,              120,                14300,              3054,
  "10B",                   0,             343,             0,              0,             0,               77,                15485,              1203,
  "10C",                   0,             358,             0,              0,             0,                0,                 2695,              1719,
  "10D",                   0,              38,            47,              0,            18,               37,                13401,               342,
  "10E",                   0,            2265,             0,            382,            28,               15,                 9052,              2779,
  "10F",                   0,             824,             0,            127,            76,                0,                13282,               743,
  "10G",                   0,             338,            40,              5,           281,               13,                 2492,               939,
  "10H",                   0,             151,             0,              0,            37,                0,                 2924,               700,
  "11A",                   0,              11,             0,              0,             6,             2111,                  317,              1532,
  "11B",                   0,              27,             0,              0,             0,                0,                  968,               702,
  "11C",                   0,               0,             0,              0,            62,                9,                 4148,              2733,
  "11D",                   0,            1108,             0,            211,           165,                0,                10756,              4030,
  "11E",                   0,            1105,             0,            190,           304,                0,                10605,              1595,
  "11F",                   0,               0,             0,             19,            70,               20,                 4327,               390,
  "11G",                   0,               0,             0,             16,            54,               56,                 6701,              2077,
  "11H",                   0,              88,             0,              0,            20,                0,                14377,              1305,
  "12A",                   0,             441,             0,             50,           123,              115,                29898,              2216,
  "12B",                   0,             404,             0,              0,            59,               55,                11845,              1397,
  "12C",                   0,             623,             0,              6,            57,                0,                18824,              1992,
  "12D",                  77,            3141,           145,            695,           172,              166,                 9555,              5101,
  "12E",                   0,             172,             0,              0,            67,                5,                 6934,               243,
  "12F",                   0,            2631,             0,            425,            74,               11,                16460,              2880,
  "12G",                   2,            3522,           319,            784,           672,                0,                29848,              9140,
  "12H",                 280,            1552,           216,            350,           551,               10,                33984,              7351
)
)

FIT <- lm(bacteria$Un.Nostocales ~ metadata$NH4)
summary(FIT)
#> 
#> Call:
#> lm(formula = bacteria$Un.Nostocales ~ metadata$NH4)
#> 
#> Residuals:
#>     Min      1Q  Median      3Q     Max 
#> -295.09 -109.93  -50.92   65.21  613.77 
#> 
#> Coefficients:
#>              Estimate Std. Error t value Pr(>|t|)    
#> (Intercept)    362.07      57.35   6.313 9.52e-09 ***
#> metadata$NH4   -56.76      14.46  -3.926 0.000167 ***
#> ---
#> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
#> 
#> Residual standard error: 183.4 on 92 degrees of freedom
#> Multiple R-squared:  0.1435, Adjusted R-squared:  0.1342 
#> F-statistic: 15.41 on 1 and 92 DF,  p-value: 0.0001668
FIT2 <- lm(bacteria$Un.Nostocales ~ metadata$BGA)
summary(FIT2)
#> 
#> Call:
#> lm(formula = bacteria$Un.Nostocales ~ metadata$BGA)
#> 
#> Residuals:
#>     Min      1Q  Median      3Q     Max 
#> -158.55 -147.86  -88.25   82.12  635.43 
#> 
#> Coefficients:
#>                Estimate Std. Error t value Pr(>|t|)  
#> (Intercept)   1.590e+02  7.570e+01   2.101   0.0384 *
#> metadata$BGA -3.998e-05  3.066e-04  -0.130   0.8966  
#> ---
#> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
#> 
#> Residual standard error: 198.1 on 92 degrees of freedom
#> Multiple R-squared:  0.0001847,  Adjusted R-squared:  -0.01068 
#> F-statistic: 0.01699 on 1 and 92 DF,  p-value: 0.8966

Created on 2019-11-06 by the reprex package (v0.3.0.9000)

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