GO analysis

Question

[Saeed]

Hello I have lists of pathways , number of genes and adj value as in bellow, How can I put all results of GO analysis (MF, BP, CC AND KEGG) pathways in a graph using ggplot2 or any package?

number of pathways are 32.

adj.Pval,          Genes ,       Pathways 


8.2e-  10  13       - Endopeptidase inhibitor activity 


8.2e-10 -  13        -Peptidase inhibitor activity 

[dthorbur]

Please provide more information. What result are you trying to highlight with this data? Is there something in the literature that you've seen that you want to replicate?

[Mark]

Post the data Saeed. Either attach a csv, upload to github, or include an example of the data.

Answer 1

[Saeed]

I manged to generate the the graph but still no pretty, I would like to make GT to each CC, MF, BP and KEGG in single.

Here is a code and data and graph are attached

ggplot(input_mat) + geom_point(aes(x = input_mat$Genes, y = input_mat$Pathways, color = input_mat$Type), size = 2) + theme_bw() + theme(axis.text.x = element_text(size=rel(1.15)), axis.title = element_text(size=rel(1.15))) + xlab("Gene number") + ylab(" GO terms") + ggtitle("Dotplot of top 30 significant GO terms") + theme(plot.title = element_text(hjust=0.5, face = "bold"))

[dthorbur]

Have you tried faceting it? Something like facet_wrap(.~Type). As an aside, you don't need to call the dataframe when you're assigning aesthetics, and for most use cases it's best practise to assign them in the main ggplot command:

ggplot(data = input_data, aes(colour = Type, x = Genes, y =  Pathways) + 
  geom_point(size = 2) +
  ...

EDIT: Just reread the post and you want them in a single plot. But the other comment remains valid, so I'll just leave it.