Barplot with coloring for different categories (classes)

README.md

How to donwload:

Click Download Zip button (topright).

How to use

Usage: Rscript barplot_with_class.R

Example: Rscript barplot_with_class.R demo.tab test.pdf

Input:

• Col 1: Categories of GO term
• Col 2: Description of the GO term
• Col 3: Percentage: here you can also use -log10(p-value) or other types of value you want.

Output:

• File name with a suffix of .pdf

Here is the figure generated using demo.tab:

barplot_with_class.R

args = commandArgs(trailingOnly=TRUE)
# test if there is at least one argument: if not, return an error
if (length(args)!=2) {
  stop("Two argument must be supplied (input file).n", call.=FALSE)
}

cc<-read.table(args[1], check.names=F, sep="\t",header=T)
### rownames(cc) <- paste(cc[,1], sprintf("%02d", cc[,2]), sep="::")
rownames(cc) = cc[,2]
cc = as.matrix(cc)

## Get category data
cat_all = cc[,c(1)]
cat_all
cat_list = unique(cat_all)
cat_list
cat <- factor(cat_all, levels = cat_list)
#head(cat)
cat_tab = table(cat)

pdf(args[2], height=2.8, width = 4)
par(mar=c(5.4,3,2.5,1), xpd=TRUE)

## Three colors are enough here.
col_list = c(rgb(152, 115, 0, max=255), rgb(90, 154, 215, max=255),
             rgb(237, 125, 49, max=255), rgb(63, 83, 35, max=255),
             rgb(255,192,0, max=255), rgb(113, 48,157, max=255),
             rgb(111,176,74, max=255), rgb(63,101,141, max=255),
             rgb(158, 72, 13, max=255), rgb(99,99,99, max=255), rgb(0, 0, 0, max=255))

### Get an vector of colors (same categories have the sample color for the bar).
col_all = c()
for(i in 1:length(cat_list)){
    num = cat_tab[i]
    cat(num, "\n")
    col_all = c(col_all, rep(col_list[i], num))
}

tab <- cbind(as.numeric(cc[,c(3)]))

rownames(tab) = rownames(cc)
colnames(tab) = c("Percentage")
#tab = t(as.matrix(cc[,c(4)])))
head(tab)
ttab <- t(tab)
x_coor <- barplot(ttab, col = col_all, las=2, ylim=c(0,100), ylab="Percentage (%)",
        border = NA, xlab = "", axes =F, beside = TRUE,
        space=c(0.25, 0.25), xlim=c(0, nrow(tab)), width=0.8)
## Add text at top of bars
text(x = x_coor + 0.5, y = ttab[1,] + 7, label = ttab[1,], pos = 3, cex = 0.8, col = col_all, srt = 45)

sum = 0

## draw the rectange under the bar for each category
ratio = 1
for(index in 1:length(cat_tab)){
    #cat(cat_tab[index], "\n")
    rect(sum*ratio, -10, (sum + cat_tab[index])*ratio, -1, col=col_list[index], border = NA)
    sum = sum + cat_tab[index]
}

### Write the category info inthe rectangle
sum = 0
for(index in 1:length(cat_tab)){
    label = names(cat_tab)[index]
    cat("Check ", index, ": ", label, "\n")
    mtext(label, side=1, at= sum+as.numeric(cat_tab[index])/2, cex = 1,
          line = -0.1, col=rgb(255,255,255, max=255))#, at= sum*1.2 + cat_tab[index]*1.2/0.5, outer=TRUE)
    sum = sum + cat_tab[index]
}


cat(sum, "\n")
axis(side=2, at = 20*(0:5))
#legend(0, 130, legend=c(" "," "," "," "," "), fill= col_ligation, border = NA, bty = "n")
dev.off()

demo.tab

Category	Description	Percentage
MF	IM08	77.6533866815935
MF	IM14	79.4809007169441
MF	IM11	82.4982000748021
CC	LC01	86.5376279999999
CC	LC09	84.5496594635102
CC	LC08	88.5778479720064
BP	LB08	82.2084337116626
BP	LB14	88.1933421109348
BP	LB06	81.1706626107194
BP	LB02	84.7519189822505