Question: Non-infinite value in violin plot
gravatar for izzy.yichao.cai
4.4 years ago by
izzy.yichao.cai170 wrote:

Hi all,

I am trying to plot a violin plot of gene expression in different categories. Since that the range of expression is quite wide, I did log transformation of the expression level. While I plot the violin plot using ggplot2, I use the following code:

data <- read.table("PATH", sep = "\t", header = FALSE)
p <- ggplot(data, aes(x=V14, y=V13, fill=V14)) + geom_violin(trim=FALSE)
p + scale_y_log10(breaks =c(0.00000001,0.0000001,0.000001,0.00001,0.0001,0.001,0.01,0.1,1,10,100,1000,10000,100000,1000000),labels = scales::trans_format("log10", scales::math_format(10^.x))) + geom_boxplot(width=0.1) + scale_x_discrete(limits=c("A","B","R","Q")) + scale_fill_manual(values=c("#99CCFF", "#E0E0E0", "#FFFF99","#FFFFFF"))

The column 13 is the expression level, while column 14 is the category of the gene. During the plotting I got message:

Removed 229 rows containing non-finite values

It is because that there are some gene with 0 expression so that it would be a non-infinite value after log transformation. But without these 0 expression values, the violin plot of 4 categories seems quite similar. However, the category R should have a lower expression level compared to other categories.

Is there any way to better display this data, while not neglect the non-infinite values? Basically, it would be ideal that reader can inform from the violin plot that:"R category, which containing some non-infinite values, has the lowest expression level compared to other categories."

Thanks a lot!!!

R • 1.8k views
ADD COMMENTlink written 4.4 years ago by izzy.yichao.cai170

Wouldn't it be an idea to just add a small scalar to your data before doing the log-transform (which would be the typical approach to avoid infinite values when logging expression)?

ADD REPLYlink written 4.4 years ago by Marge300
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1933 users visited in the last hour