Hello everybody 
What function, or steps should (do u recommend) I perform so that the arrows and circles (the variables of my graph) are more distributed, more separated? All the variables on the graph look very close together, which makes this statistic very difficult to understand.
Metadata <- data.frame (tibble::tribble(
~SampleID, ~Month, ~Dissolved.oxygen, ~pH,
"1A", "July", 4.24, 9.94,
"1B", "July", 2.58, 10.06,
"1C", "July", 2.85, 9.98,
"1D", "August", 3.81, 9.07,
"1E", "August", 2.64, 8.99,
"1F", "August", 4.61, 8.93,
"1G", "September", 5.74, 9.24,
"1H", "September", 3.69, 9.32,
"2A", "July", 4.24, 9.94,
"2B", "July", 2.66, 10,
"2C", "July", 2.85, 9.98,
"2D", "August", 3.81, 9.07,
"2E", "August", 2.64, 8.99,
"2F", "August", 4.61, 8.93,
"2G", "September", 5.74, 9.24,
"2H", "September", 3.69, 9.32,
"3A", "July", 2.51, 10.04,
"3B", "July", 2.66, 10,
"3C", "July", 3.14, 10,
"3D", "August", 2.92, 9.06,
"3E", "August", 1.83, 8.99,
"3F", "August", 1.82, 8.92,
"3G", "September", 3.02, 9.18,
"3H", "September", 3.3, 9.32,
"4A", "July", 2.51, 10.04,
"4B", "July", 3.04, 9.96,
"4C", "July", 2.85, 9.98,
"4D", "August", 2.92, 9.06,
"4E", "August", 1.83, 8.99,
"4F", "August", 1.82, 8.92,
"4G", "September", 3.02, 9.18,
"4H", "September", 3.3, 9.32,
"5A", "July", 4.24, 9.94,
"5B", "July", 3.04, 9.96,
"5C", "July", 2.85, 9.98,
"5D", "August", 3.81, 9.07,
"5E", "August", 2.64, 8.99,
"5F", "August", 4.61, 8.93,
"5G", "September", 5.74, 9.24,
"5H", "September", 3.69, 9.32,
"6A", "July", 4.24, 9.94,
"6B", "July", 2.09, 9.95,
"6C", "July", 2.98, 10.09,
"6D", "August", 3.81, 9.07,
"6E", "August", 1.83, 8.99,
"6F", "August", 1.82, 8.92,
"6G", "September", 3.02, 9.18,
"6H", "September", 3.3, 9.32,
"7A", "July", 2.51, 10.04,
"7B", "July", 2.09, 9.95,
"7C", "July", 2.98, 10.09,
"7D", "August", 8.17, 9.04,
"7E", "August", 2.63, 9,
"7F", "September", 7.69, 9.53,
"7G", "September", 3.07, 9.31,
"7H", "September", 3.7, 9.14,
"8A", "July", 2.51, 10.04,
"8B", "July", 3.04, 9.96,
"8C", "July", 2.18, 9.97,
"8D", "August", 8.17, 9.04,
"8E", "August", 2.63, 9,
"8F", "September", 7.69, 9.53,
"8G", "September", 3.07, 9.31,
"8H", "September", 3.7, 9.14,
"9A", "July", 2.58, 10.06,
"9B", "July", 2.09, 9.95,
"9C", "July", 2.18, 9.97,
"9D", "August", 2.16, 8.96,
"9E", "August", 1.7, 9.02,
"9F", "September", 6.8, 9.51,
"9G", "September", 1.95, 9.39,
"9H", "September", 4.28, 8.85,
"10A", "July", 2.58, 10.06,
"10B", "July", 2.09, 9.95,
"10C", "July", 2.98, 10.09,
"10D", "August", 2.16, 8.96,
"10E", "August", 1.7, 9.02,
"10F", "September", 6.8, 9.51,
"10G", "September", 1.95, 9.39,
"10H", "September", 4.28, 8.85,
"11A", "July", 2.66, 10,
"11B", "July", 3.14, 10,
"11C", "July", 2.18, 9.97,
"11D", "August", 8.17, 9.04,
"11E", "August", 2.63, 9,
"11F", "September", 7.69, 9.53,
"11G", "September", 3.07, 9.31,
"11H", "September", 3.7, 9.14,
"12A", "July", 2.66, 10,
"12B", "July", 3.14, 10,
"12C", "August", 2.92, 9.06,
"12D", "August", 2.16, 8.96,
"12E", "August", 1.7, 9.02,
"12F", "September", 6.8, 9.51,
"12G", "September", 1.95, 9.39,
"12H", "September", 4.28, 8.85
)
)
Familia <- data.frame (tibble::tribble(
~index, ~K00001, ~K00002, ~K00003, ~K00004, ~K00005, ~K00006, ~K00007,
"1A", 10861L, 15L, 10972L, 526L, 84L, 0L, 412L,
"1B", 2784L, 63L, 3141L, 130L, 311L, 0L, 72L,
"1C", 3438L, 110L, 6882L, 335L, 92L, 0L, 188L,
"1D", 8032L, 42L, 9491L, 417L, 394L, 0L, 49L,
"1E", 12804L, 89L, 12584L, 3441L, 513L, 0L, 255L,
"1F", 11037L, 242L, 12637L, 1111L, 746L, 53L, 1491L,
"1G", 963L, 21L, 1629L, 153L, 207L, 0L, 304L,
"1H", 7573L, 282L, 7992L, 276L, 1039L, 0L, 684L,
"2A", 10475L, 287L, 13421L, 1159L, 2027L, 9L, 1378L,
"2B", 4922L, 266L, 7832L, 603L, 1436L, 3L, 444L,
"2C", 4314L, 64L, 5734L, 316L, 734L, 0L, 658L,
"2D", 6916L, 66L, 7313L, 233L, 597L, 8L, 519L,
"2E", 6779L, 71L, 12027L, 2114L, 605L, 2L, 392L,
"2F", 2799L, 28L, 3964L, 543L, 258L, 0L, 342L,
"2G", 7174L, 193L, 11741L, 306L, 1173L, 2L, 875L,
"2H", 10706L, 220L, 9147L, 1483L, 878L, 13L, 742L,
"3A", 8358L, 289L, 13925L, 554L, 694L, 0L, 563L,
"3B", 375L, 9L, 1112L, 65L, 653L, 0L, 18L,
"3C", 1991L, 10L, 2296L, 200L, 16L, 0L, 218L,
"3D", 2514L, 6L, 3058L, 184L, 50L, 0L, 0L,
"3E", 3763L, 17L, 4350L, 1085L, 272L, 0L, 246L,
"3F", 2532L, 56L, 3193L, 239L, 132L, 0L, 474L,
"3G", 3116L, 86L, 3634L, 276L, 293L, 0L, 498L,
"3H", 338L, 0L, 356L, 2L, 6L, 0L, 21L,
"4A", 21675L, 659L, 31368L, 2746L, 4167L, 11L, 2480L,
"4B", 3963L, 86L, 4996L, 330L, 733L, 0L, 248L,
"4C", 1361L, 10L, 1953L, 95L, 202L, 0L, 231L,
"4D", 5671L, 114L, 7134L, 529L, 571L, 10L, 591L,
"4E", 6300L, 99L, 7649L, 748L, 723L, 0L, 681L,
"4F", 463L, 0L, 726L, 8L, 8L, 0L, 1L,
"4G", 6905L, 256L, 17256L, 1059L, 1092L, 0L, 288L,
"4H", 27333L, 464L, 29402L, 1458L, 1904L, 29L, 1242L,
"5A", 11105L, 105L, 17428L, 4056L, 886L, 5L, 17L,
"5B", 5289L, 814L, 5732L, 366L, 121L, 0L, 373L,
"5C", 1960L, 14L, 1716L, 23L, 43L, 0L, 73L,
"5D", 2649L, 34L, 3039L, 336L, 254L, 0L, 130L,
"5E", 4900L, 61L, 9775L, 501L, 170L, 0L, 602L,
"5F", 9136L, 113L, 9531L, 403L, 410L, 7L, 389L,
"5G", 6123L, 66L, 7662L, 1683L, 471L, 0L, 45L,
"5H", 6586L, 104L, 13675L, 1920L, 598L, 0L, 206L,
"6A", 11647L, 231L, 17360L, 1165L, 1979L, 0L, 2006L,
"6B", 11228L, 204L, 12118L, 1323L, 605L, 0L, 250L,
"6C", 2950L, 58L, 4320L, 254L, 396L, 0L, 506L,
"6D", 4130L, 77L, 4398L, 316L, 318L, 0L, 333L,
"6E", 4864L, 46L, 6386L, 631L, 520L, 0L, 642L,
"6F", 6534L, 133L, 8273L, 778L, 693L, 36L, 977L,
"6G", 4033L, 23L, 8851L, 1554L, 849L, 2L, 27L,
"6H", 13459L, 310L, 19110L, 2677L, 2282L, 6L, 1199L,
"7A", 17920L, 336L, 19100L, 475L, 774L, 0L, 97L,
"7B", 1838L, 374L, 4909L, 39L, 63L, 0L, 174L,
"7C", 1883L, 18L, 4695L, 25L, 246L, 0L, 97L,
"7D", 6912L, 183L, 10446L, 549L, 2371L, 0L, 760L,
"7E", 10849L, 234L, 11701L, 681L, 884L, 10L, 476L,
"7F", 11940L, 128L, 13971L, 515L, 623L, 0L, 333L,
"7G", 3213L, 48L, 3564L, 1091L, 404L, 0L, 29L,
"7H", 2352L, 47L, 4354L, 552L, 197L, 0L, 53L,
"8A", 8872L, 132L, 12609L, 646L, 1406L, 5L, 1062L,
"8B", 14646L, 374L, 16749L, 1092L, 995L, 8L, 1180L,
"8C", 1856L, 28L, 2321L, 66L, 189L, 0L, 370L,
"8D", 15306L, 355L, 17509L, 1318L, 2402L, 0L, 1456L,
"8E", 7536L, 346L, 9438L, 956L, 1009L, 0L, 1360L,
"8F", 16096L, 275L, 18590L, 928L, 834L, 25L, 1395L,
"8G", 12809L, 178L, 16649L, 2605L, 2075L, 0L, 163L,
"8H", 14535L, 148L, 15388L, 601L, 792L, 0L, 638L,
"9A", 4593L, 515L, 7812L, 444L, 91L, 0L, 252L,
"9B", 9887L, 747L, 11876L, 488L, 141L, 0L, 804L,
"9C", 2253L, 14L, 3415L, 224L, 116L, 0L, 3L,
"9D", 19255L, 725L, 20103L, 2958L, 3813L, 0L, 1262L,
"9E", 27151L, 166L, 22181L, 703L, 548L, 0L, 1016L,
"9F", 9634L, 496L, 13486L, 1399L, 993L, 18L, 1500L,
"9G", 3274L, 62L, 10840L, 567L, 261L, 15L, 169L,
"9H", 1482L, 187L, 5646L, 346L, 3799L, 0L, 30L,
"10A", 5624L, 115L, 6239L, 483L, 473L, 0L, 239L,
"10B", 2402L, 33L, 3523L, 316L, 244L, 0L, 264L,
"10C", 3093L, 57L, 3627L, 170L, 390L, 0L, 263L,
"10D", 3122L, 59L, 6064L, 162L, 2763L, 0L, 238L,
"10E", 4556L, 69L, 5486L, 477L, 553L, 0L, 488L,
"10F", 2668L, 64L, 4038L, 316L, 390L, 0L, 677L,
"10G", 2260L, 25L, 2754L, 130L, 188L, 0L, 129L,
"10H", 1760L, 82L, 1903L, 94L, 138L, 0L, 119L,
"11A", 2332L, 6L, 1815L, 44L, 403L, 0L, 3L,
"11B", 705L, 2L, 944L, 15L, 16L, 0L, 1L,
"11C", 6343L, 100L, 7175L, 214L, 597L, 0L, 53L,
"11D", 10106L, 311L, 11605L, 1142L, 1158L, 0L, 1165L,
"11E", 5818L, 27L, 6479L, 1194L, 311L, 7L, 301L,
"11F", 1983L, 148L, 4367L, 329L, 53L, 1L, 135L,
"11G", 3041L, 59L, 6673L, 526L, 95L, 0L, 53L,
"11H", 5489L, 659L, 12844L, 1274L, 187L, 0L, 823L,
"12A", 3857L, 184L, 5806L, 264L, 508L, 0L, 533L,
"12B", 5121L, 168L, 6016L, 263L, 722L, 0L, 165L,
"12C", 3289L, 70L, 4528L, 122L, 457L, 0L, 710L,
"12D", 13741L, 241L, 15175L, 4650L, 864L, 14L, 239L,
"12E", 5806L, 286L, 6275L, 674L, 42L, 0L, 380L,
"12F", 8220L, 148L, 9672L, 911L, 767L, 15L, 943L,
"12G", 23915L, 378L, 30151L, 6820L, 2273L, 29L, 1189L,
"12H", 12224L, 1094L, 16467L, 2183L, 2088L, 11L, 1165L
)
)
attach(Familia)
Familia <- Familia[,-1]
rownames(Familia) <- SampleID
#> Error in eval(expr, envir, enclos): objeto 'SampleID' no encontrado
attach(Metadata)
Metadata <- Metadata[,-1]
rownames(Metadata) <- SampleID
#remove the rare microbes. It keeps only the microbes that are present in at least 10% of the samples
dim(Familia)
#> [1] 96 7
Familia <- Familia[,colMeans(Familia) >=.1]
dim(Familia)
#> [1] 96 7
library(vegan)
#> Loading required package: permute
#> Loading required package: lattice
#> This is vegan 2.5-6
rda_object <- vegan::rda(Familia, Metadata[,1:3], scale=TRUE)
plot(rda_object)
library(BiodiversityR)
#> Loading required package: tcltk
#> Loading required package: vegan3d
#> Loading required package: rgl
#> BiodiversityR 2.11-3: Use command BiodiversityRGUI() to launch the Graphical User Interface;
#> to see changes use BiodiversityRGUI(changeLog=TRUE, backward.compatibility.messages=TRUE)
PCAsignificance(rda_object, axes=8)
#> 1 2 3 4
#> eigenvalue 3.993885 0.7821051 0.6843581 0.5003179
#> percentage of variance 60.543381 11.8559461 10.3741972 7.5843279
#> cumulative percentage of variance 60.543381 72.3993275 82.7735247 90.3578526
#> broken-stick percentage 37.040816 22.7551020 15.6122449 10.8503401
#> broken-stick cumulative % 37.040816 59.7959184 75.4081633 86.2585034
#> % > bs% 1.000000 0.0000000 0.0000000 0.0000000
#> cum% > bs cum% 1.000000 1.0000000 1.0000000 1.0000000
#> 5 6 7
#> eigenvalue 0.3662658 0.2223026 0.04749837
#> percentage of variance 5.5522294 3.3698894 0.72002862
#> cumulative percentage of variance 95.9100820 99.2799714 100.00000000
#> broken-stick percentage 7.2789116 4.4217687 2.04081633
#> broken-stick cumulative % 93.5374150 97.9591837 100.00000000
#> % > bs% 0.0000000 0.0000000 0.00000000
#> cum% > bs cum% 1.0000000 1.0000000 0.00000000
library(devtools)
#> Loading required package: usethis
#>
#> Attaching package: 'devtools'
#> The following object is masked from 'package:permute':
#>
#> check
library(ggord)
Metadata$Month <- factor(Metadata$Month,
levels = c("July", "August", "September"))
Familia <- Metadata$Month
bg <- c("#ffebee","#ab47bc", "#3949ab","#ffcdd2","#ef9a9a","#e57373","#ef5350","#f44336","#e31a1c")
# axes 1 & 2
plot(rda_object, type = "n", scaling=3, display = "sites", xlab = "RDA1 (24.68%)", ylab = "RDA2 (21.74%)")
points(rda_object, display="sites", pch=21, cex=1.7, col="gray32", scaling=3)
points(rda_object, display="sites", pch=21, cex=1.7, col="gray32", scaling=3, bg=bg[Familia])
text(rda_object, scaling=3, display="bp", col="#e31a1c", cex=1, face ="bold")
#> Warning in arrows(0, 0, pts[, 1], pts[, 2], length = head.arrow, ...): "face" is
#> not a graphical parameter
#> Warning in strwidth(labels, ...): "face" is not a graphical parameter
#> Warning in strheight(labels, ...): "face" is not a graphical parameter
#> Warning in text.default(pts, labels = rownames(pts), ...): "face" is not a
#> graphical parameter
legend("bottomright", legend=levels(Familia), bty="n",xpd= FALSE, col="gray32", pch=21, cex=1.7, pt.bg=bg)
Created on 2021-06-24 by the reprex package (v0.3.0)
In this short example looks good, but this is the original graph.
