Question: Dotplot for filtered pathways result
6
gravatar for Leite
21 months ago by
Leite1.1k
São Paulo - Brazil - Unifesp
Leite1.1k 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 3 months ago by sara-hammoudeh10 • written 21 months ago by Leite1.1k
1

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

ADD REPLYlink written 21 months ago by Benn8.0k

@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 21 months ago by Leite1.1k
1

of course it is possible, try msigdbr + clusterProfiler

ADD REPLYlink written 21 months ago by Guangchuang Yu2.4k
4

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

ADD REPLYlink modified 27 days ago • written 21 months ago by Leite1.1k

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

ADD REPLYlink written 16 months ago by sutturka170

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

I hope you can generate your graphics

S1.csv

ADD REPLYlink modified 16 months ago • written 16 months ago by Leite1.1k

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

ADD REPLYlink written 14 months ago by moloneyger0

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 ?

ADD REPLYlink written 3 months ago by sunnykevin97140
1

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

ADD REPLYlink written 3 months ago by sara-hammoudeh10

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

ADD REPLYlink written 11 months ago by alepaolini8610

Hey guys,

New Link, enjoy.

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

ADD REPLYlink written 11 months ago by Leite1.1k
3

Hi there,

Would you be able to reupload the S1 file?

Thanks in advance.

ADD REPLYlink written 6 months ago by Andiamo30

I will try to post the file on github

ADD REPLYlink written 4 weeks ago by Leite1.1k
2

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

ADD REPLYlink modified 27 days ago • written 27 days ago by Leite1.1k

Thank you so much!!!

ADD REPLYlink written 27 days ago by anshulmbi30

please provide new link asap!!

ADD REPLYlink written 27 days ago by anshulmbi30

Link dont work? here its work fine

ADD REPLYlink written 27 days ago by Leite1.1k
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