Question: Dotplot for filtered pathways result
0
gravatar for Leite
4 weeks ago by
Leite320
Leite320 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 4 weeks ago by RamRS20k • written 4 weeks ago by Leite320
1

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

ADD REPLYlink written 4 weeks ago by b.nota6.1k

@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 4 weeks ago by Leite320
1

of course it is possible, try msigdbr + clusterProfiler

ADD REPLYlink written 4 weeks ago by Guangchuang Yu2.1k

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 25 days ago • written 25 days ago by Leite320
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