DAVID gene ontology using dotplot

Question

[alepaolini86]

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

Answer 1

[Leite]

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

[georgians]

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

[Leite]

I will try to post the file on github

[georgians]

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

[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