DAVID gene ontology using dotplot
1
1
Entering edit mode
5.0 years ago
alepaolini86 ▴ 10

I have a list of gene that I have put in DAVID analysis. I saved the Kegg pathway, biological process etc results in .csv file. I desire to represent the analysis with dotplot (see image) in R starting with .csv file from DAVID tools. Is there a R script that I can use? Thanks ! enter image description here

R gene DAVID dotplot • 4.5k views
ADD COMMENT
2
Entering edit mode
5.0 years ago
Leite ★ 1.3k

Hey alepaolini86,

You may notice that I asked this same question a while ago, and in that question I put the answer with the code, as you can see here.

A: Dotplot for filtered pathways result

note that in my code I used the function facet_grid(Group ~ .) because I wanted to split in groups.

As you can see in my example, that was recently published

Sem-Titulo-1.png

ADD COMMENT
0
Entering edit mode

Hi, Could you please add link here for your example file, current link is not working. Thank you!!

ADD REPLY
0
Entering edit mode

I will try to post the file on github

ADD REPLY
0
Entering edit mode

Thank you for your reply. Could you please add link asap as its urgent!!!!

ADD REPLY
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 2386 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6