DAVID gene ontology using dotplot
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24 months 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 • 2.3k views
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24 months ago
Leite ★ 1.2k

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

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I will try to post the file on github

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Hey

library(ggplot2)
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