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Dotplot for filtered pathways result

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
• 26,262 views • link
written by Leite Leite

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

• 1 views • link
written by Benn Benn

@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.

• 1 views • link
written by Leite Leite

of course it is possible, try msigdbr + clusterProfiler

• 1 views • link
written by Guangchuang Yu Guangchuang Yu

Hey

S1 = https://raw.githubusercontent.com/GiuseppeLeite/Data/master/S1.csv

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

• 1 views • link
written by Leite Leite

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

• 0 views • link
written by sutturka sutturka

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

I hope you can generate your graphics

S1.csv

• 0 views • link
written by Leite Leite

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

• 0 views • link
written by moloneyger • moloneyger

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 ?

• 0 views • link
written by sunnykevin97 sunnykevin97

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

• 0 views • link
written by alepaolini86 • alepaolini86

Hi there,

Would you be able to reupload the S1 file?

Thanks in advance.

• 0 views • link
written by Andiamo • Andiamo

I will try to post the file on github

• 0 views • link
written by Leite Leite

Link dont work? here its work fine

• 0 views • link
written by Leite Leite

Hey

S1 = https://raw.githubusercontent.com/GiuseppeLeite/Data/master/S1.csv

library(ggplot2)
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

• 0 views • link
written by Leite Leite

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

• 0 views • link
written by sara-hammoudeh • sara-hammoudeh

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