Question: Dotplot for filtered pathways result
0
gravatar for Leite
5 months ago by
Leite410
Leite410 wrote:

I have a list of pathways that I have filtered from MSigDB and would like to represent them in graphs like this one. Showing the value of FDR and the number of SDRs found in each of the groups (survivors and not)

I've tried importing into the R and then using the clusterProfiler as well as ggplot2! But I could not find a way to do that.

Graph Example

Example of my list of pathways

Best regards,

Leite

ADD COMMENTlink modified 5 months ago by RamRS22k • written 5 months ago by Leite410
1

Try doing the analysis from start in clusterProfiler and follow the manual.

ADD REPLYlink written 5 months ago by Benn7.0k

@b.nota thank you for your answer, but I need to represent very specific pathways and doing the manual I believe would not be possible.

ADD REPLYlink written 5 months ago by Leite410
1

of course it is possible, try msigdbr + clusterProfiler

ADD REPLYlink written 5 months ago by Guangchuang Yu2.2k
1

Hey all I managed to do using the ggplot2

data <- read.csv("S1.csv", sep =";", header = TRUE, stringsAsFactors = FALSE)
 library("ggplot2")
 S1<- ggplot(data, aes(x="Groups", y=Pathways, size=DEGs, color=FDR)) + geom_point(alpha = 0.8) + facet_grid(Group ~ .) + theme_classic()
 S1

 S1 = S1+scale_color_gradient(low = "red2",  high = "mediumblue", space = "Lab", limit = c(0.000000000000000000000000000000000000000000000004, 0.03))
S1+scale_size(range = c(2, 8))
S1
ADD REPLYlink modified 5 months ago • written 5 months ago by Leite410

Great. Can you please add snippet of S1.csv file for reference?

ADD REPLYlink written 5 weeks ago by sutturka150

Sure enough, I attached the table S1.csv to my drive.

I hope you can generate your graphics

S1.csv

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by Leite410
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