multiple box plot with posthoc test result as letters

[bioinfonext]

@technocrat,

I have added data detail with str command, it says this is also a data frame after reading the file by read.table in R.

Many thanks,

[technocrat]

multcompBoxplot(SampleType ~ Cd, data = bpdata[, c(1, 6)])

Cd is the seventh column, not the sixth. Use Cd or change data argument to

multcompBoxplot(SampleType ~ Cd, data = bpdata[, c(1, 7)])

[bioinfonext]

Thanks, but again some error;
code;

suppressPackageStartupMessages({
  library(multcompView)
})

bpdata <- read.table("Box.plot.chemical.txt", sep="\t", header=TRUE, row.names= NULL)
str(bpdata)


pdf("test2.plot.pdf", width = 10, height = 8)

multcompBoxplot(SampleType ~ Cd, data = bpdata[, c(1, 7)])
dev.off();

Error in oldClass(stats) <- cl :
  adding class "factor" to an invalid object
Calls: multcompBoxplot ... boxplot -> boxplot.formula -> boxplot -> boxplot.defa                                                                                        ult
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Execution halted

Many thanks

[technocrat]

Look, it's very hard to eyeball this stuff. See the FAQ: How to do a minimal reproducible example reprex for beginners for how to provide representative data that can be cut and pasted.

[bioinfonext]

@technocrat,

I have pasted here reproducible code from a file;

SampleType	Bacteria	Fe	P	Ca
D_M_1Chemical	7,00,000	1,40,67,895	3,80,000	69,000
D_M_2Farm	3,16,680	93,11,160	2,50,000	26,000
D_M_3ChemicalFarm	3,13,010	84,22,355	4,60,000	30,000
D_M_1Chemical	3,74,535	92,59,900	2,80,000	33,000
D_M_2Farm	3,70,000	1,69,52,360	3,20,000	72,000
D_M_3ChemicalFarm	4,62,480	1,05,26,390	3,60,000	64,000
D_M_1Chemical	3,74,860	83,78,655	2,90,000	49,000
D_M_2Farm	3,81,900	94,68,550	3,90,000	73,000
D_M_3ChemicalFarm	2,00,000	57,83,980	4,40,000	61,000
D_M_1Chemical	2,24,125	80,77,105	6,00,000	89,000
D_M_2Farm	1,90,810	81,54,005	6,00,000	61,000
D_M_3ChemicalFarm	1,77,050	83,33,120	6,00,000	69,000
D_M_1Chemical	2,70,000	52,77,265	2,00,000	34,000
D_M_2Farm	4,03,380	92,37,105	4,90,000	80,000
D_M_3ChemicalFarm	3,72,530	1,06,24,735	4,80,000	57,000
D_M_1Chemical	2,61,215	62,28,160	3,40,000	37,000
D_M_2Farm	7,50,000	1,62,58,720	4,40,000	80,000
D_M_3ChemicalFarm	6,33,895	1,09,52,305	3,80,000	54,000
D_M_1Chemical	5,83,367	1,03,83,383	3,10,000	53,000
D_M_2Farm	6,53,945	1,01,48,210	3,80,000	48,000
D_M_3ChemicalFarm	5,70,000	1,10,00,000	1,80,000	1,70,000
D_M_1Chemical	5,20,000	2,70,00,000	1,30,000	1,90,000
D_M_2Farm	5,40,000	2,10,00,000	2,50,000	1,40,000
D_M_3ChemicalFarm	4,70,000	1,00,00,000	1,10,000	70,000
D_M_1Chemical	6,40,000	1,30,00,000	1,70,000	90,000
D_M_2Farm	7,70,000	1,70,00,000	2,30,000	1,20,000
D_M_3ChemicalFarm	7,20,000	1,50,00,000	1,20,000	1,70,000
D_B_1Chemical	6,20,000	1,20,00,000	98,000	74,000
D_B_2Farm	9,40,000	2,95,82,000	1,90,000	46,000
D_B_3ChemicalFarm	9,52,400	2,71,86,525	2,10,000	67,000
D_B_1Chemical	5,03,300	1,11,40,225	85,000	24,000

So the first column is Sampletype and others are variable.

Many thanks,

[technocrat]

@bioinfonext

reproducible code

Thanks. I'll look at it, but this is what reproducible code looks like (cut-and-paste) using dput(your_data.frame)

dat <- structure(list(
  SampleType =
    c("D_M_1Chemical", "D_M_2Farm", "D_M_3ChemicalFarm", "D_M_1Chemical", "D_M_2Farm", "D_M_3ChemicalFarm", "D_M_1Chemical", "D_M_2Farm", "D_M_3ChemicalFarm", "D_M_1Chemical", "D_M_2Farm", "D_M_3ChemicalFarm", "D_M_1Chemical", "D_M_2Farm", "D_M_3ChemicalFarm", "D_M_1Chemical", "D_M_2Farm", "D_M_3ChemicalFarm", "D_M_1Chemical", "D_M_2Farm", "D_M_3ChemicalFarm", "D_M_1Chemical", "D_M_2Farm", "D_M_3ChemicalFarm", "D_M_1Chemical", "D_M_2Farm", "D_M_3ChemicalFarm", "D_B_1Chemical", "D_B_2Farm", "D_B_3ChemicalFarm", "D_B_1Chemical"),
  Bacteria =
    c(7e+05, 316680, 313010, 374535, 370000, 462480, 374860, 381900, 2e+05, 224125, 190810, 177050, 270000, 403380, 372530, 261215, 750000, 633895, 583367, 653945, 570000, 520000, 540000, 470000, 640000, 770000, 720000, 620000, 940000, 952400, 503300),
  Fe =
    c(14067895, 9311160, 8422355, 9259900, 16952360, 10526390, 8378655, 9468550, 5783980, 8077105, 8154005, 8333120, 5277265, 9237105, 10624735, 6228160, 16258720, 10952305, 10383383, 10148210, 1.1e+07, 2.7e+07, 2.1e+07, 1e+07, 1.3e+07, 1.7e+07, 1.5e+07, 1.2e+07, 29582000, 27186525, 11140225),
  P =
    c(380000, 250000, 460000, 280000, 320000, 360000, 290000, 390000, 440000, 6e+05, 6e+05, 6e+05, 2e+05, 490000, 480000, 340000, 440000, 380000, 310000, 380000, 180000, 130000, 250000, 110000, 170000, 230000, 120000, 98000, 190000, 210000, 85000),
  Ca =
    c(69000, 26000, 30000, 33000, 72000, 64000, 49000, 73000, 61000, 89000, 61000, 69000, 34000, 80000, 57000, 37000, 80000, 54000, 53000, 48000, 170000, 190000, 140000, 70000, 90000, 120000, 170000, 74000, 46000, 67000, 24000)),
  class =
    c("spec_tbl_df", "tbl_df", "tbl", "data.frame"),
  row.names =
    c(NA, -31L), spec = structure(list(cols = list( SampleType = structure(list(),
  class =
    c("collector_character", "collector")), Bacteria = structure(list(),
  class =
    c("collector_double", "collector")), Fe = structure(list(),
  class =
    c("collector_double", "collector")), P = structure(list(),
  class =
    c("collector_double", "collector")), Ca = structure(list(),
  class =
    c("collector_double", "collector"))), default = structure(list(),
  class =
    c("collector_guess", "collector")), skip = 1L),
  class = "col_spec"))