Scatter plot for GSEA results analysis
2
4
Entering edit mode
6.2 years ago

Hi All,

I really like fig 5A in this paper:

http://www.nature.com/nbt/journal/v31/n1/full/nbt.2450.html

It neatly displays result of the GSEA analysis with an indication of gene set size and P-value. Can anyone help me figure out how to make a graph like this given gene set + enrichment score + P-value + gene set size?

Thanks

Abdul

RNA-Seq • 6.2k views
ADD COMMENT
0
Entering edit mode

This post was cited in:

Programming of Schwann Cells by Lats1/2-TAZ/YAP Signaling Drives Malignant Peripheral Nerve Sheath Tumorigenesis . Cancer Cell. Volume 33, Issue 2, p292–308.e7, 12 February 2018 https://doi.org/10.1016/j.ccell.2018.01.005

ADD REPLY
8
Entering edit mode
5.5 years ago
siabadaba ▴ 100

Hi, I've run into your question while looking for something else. This gave me great idea to show my own analysis. I've prepared this fig-5A-like plot and I thought to share it. Here is the result picture:

http://imgur.com/XC9dWXJ GSEA Scatter plot

And here is the code (in R):

# Preparing data
data <- data.frame(Gene_set=c("Gene_set1", "Gene_set2", "Gene_set3", "Gene_set4", "Gene_set5"),
                   NES=runif(5, -3, 3),
                   FDR_q.val=runif(5,0,1),
                   No_of_significant_genes=runif(5, 1, 100))

# Plotting
library(ggplot2) 
p <- ggplot(data, aes(NES, Gene_set))
p + geom_point(aes(colour=FDR_q.val, size=No_of_significant_genes)) +
    scale_color_gradientn(colours=rainbow(4), limits=c(0, 1)) +
    geom_vline(xintercept=0, size=0.5, colour="gray50") +
    theme(panel.background=element_rect(fill="gray95", colour="gray95"),
          panel.grid.major=element_line(size=0.25,linetype='solid', colour="gray90"), 
          panel.grid.minor=element_line(size=0.25,linetype='solid', colour="gray90"),
          axis.title.y=element_blank()) +
    expand_limits(x=c(-3,3)) +
    scale_x_continuous(breaks=c(-3,-2,-1,0,1,2,3)) +
    scale_y_discrete(limits=rev(data$Gene_set))
ADD COMMENT
0
Entering edit mode

Thank you so much for sharing the code! It's awesome!

ADD REPLY
0
Entering edit mode

I don't understand what the "number of significant genes" corresponds to in the GSEA results. Is it the number of genes marked as "core enrichment"?

ADD REPLY
2
Entering edit mode
6.2 years ago
roy.granit ▴ 880

You can get such nice plots using clusterProfiler, as seen here:

http://www.r-bloggers.com/david-functional-analysis-with-clusterprofiler/

ADD COMMENT

Login before adding your answer.

Traffic: 2257 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6