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how to get a readable scale on a particular R plot

Hello,

I'm having difficulties to get a plot with a readable scale.

I have plotted transcriptomic data using R with package EMA. However 'genes names' (ordinate axis) are written too big and I can't see all gene names. I would like to have one gene name per compartment.

plot picture

Here is my code:

clustering.plot(tree= c.sample, tree.sup=c.gene, data=tpm.100,
                dendro=TRUE, dendro.sup=TRUE, names=TRUE, names.sup=TRUE, names.dist=TRUE, trim.heatmap=0.99)

clustering.plot(tree= c.sample, tree.sup=c.gene, data=tpm.100,
                legend=FALSE, legend.pos="bottomright",
                dendro=FALSE, dendro.sup=FALSE,names.sup=TRUE, names.dist=TRUE,trim.heatmap=0.99)

I have read EMA package documentation to play with different options without success.

I'm new with R, there should be some obvious things i'm missing

Thank you for your help

r ema plot transcriptomic
• 2,443 views • link
written by vmicrobio vmicrobio

what is the size of tpm.100 ? can you try removing trim.heatmap function in the code?

• 0 views • link
written by cpad0112 cpad0112

thank you for your comment. tmp.100 is a 15x87 table (including one line and one column of headers). Without trim.heatmap I get the same graph.

• 0 views • link
written by vmicrobio vmicrobio

1 answer

It was recommanded to me to use pheatmap package (https://stackoverflow.com/questions/63225729/how-to-get-a-readable-scale-on-a-particular-r-plot)

Here is what I get: 

install.packages("pheatmap")
library(pheatmap)

# load data and subset
data=read.table("/Users/vmicrobio/Desktop/tpm.100.txt",sep="\t",header=TRUE,row.names = 1 )
head(data)

# data.matrix()
data_subset <- as.matrix((data), threshold = 10, p=0.2)
tpm=data.frame(data_subset)
tpm.log <- log2(tpm[,]+1)

# normalization
cal_z_score <- function(x){
  (x - mean(x)) / sd(x)
}
tpm.log_norm <- t(apply(tpm.log, 1, cal_z_score))

# heatmap
pheatmap(tpm.log_norm, main="test norm", fontsize_row=6, filename="/Users/vmicrobio/Desktop/heatmap_test.pdf")

plot

• 0 views • link
written by vmicrobio vmicrobio

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