Dotplot for filtered pathways result
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3.9 years ago
Leite ★ 1.2k

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 DEGs 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

pathways ggplot2 clusterProfiler r dotplot • 15k views
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Try doing the analysis from start in clusterProfiler and follow the manual.

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@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.

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of course it is possible, try msigdbr + clusterProfiler

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Hey

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

S1 = S1+scale_color_gradient(low = "red2",  high = "mediumblue", space = "Lab", limit = c(0.000000000000000007,
0.002))
S1+scale_size(range = c(2, 8))
S1


Best regards,

Leite

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

I hope you can generate your graphics

S1.csv

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The link to the S1 file is broken, could you reload it? Thanks.

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HI Leite, I tried to dotplot for my data, it doesn't work out using cluster profiler. Can you show off your data in a table format, wish to plot the same graph as you shown above. How to calculate FDR ?

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Hello, Can you please reupload or describe the structure of the input .csv file? I would truly appreciate your help.

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The link to the S1 file is broken, could you reload it again? Thanks.

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Hey guys,

https://www.4shared.com/s/fmJvXsSzcea

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Hi there,

Would you be able to reupload the S1 file?

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I will try to post the file on github

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Hey

library(ggplot2)
S1<- ggplot(data, aes(x= Group, y=Pathways, size=DEGs, color=FDR, group=Group)) + geom_point(alpha = 0.8) +
theme_classic()
S1

S1 = S1+scale_color_gradient(low = "red2",  high = "mediumblue", space = "Lab", limit = c(0.000000000000000007,
0.002))
S1+scale_size(range = c(2, 8))
S1


Best regards,

Leite

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Thank you so much!!!

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Link dont work? here its work fine