Dotplot for filtered pathways result

Question

[Leite]

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

[Benn]

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

[Leite]

@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.

[Guangchuang Yu]

of course it is possible, try msigdbr + clusterProfiler

[Leite]

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

[sutturka]

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

[Leite]

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

I hope you can generate your graphics

S1.csv

[moloneyger]

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

[sunnykevin97]

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 ?

[sara-hammoudeh]

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

[alepaolini86]

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

[Leite]

Hey guys,

New Link, enjoy.

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

[Andiamo]

Hi there,

Would you be able to reupload the S1 file?

Thanks in advance.

[Leite]

I will try to post the file on github

[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

[georgians]

Thank you so much!!!

[georgians]

please provide new link asap!!

[Leite]

Link dont work? here its work fine