How to make a plot with gProfileR results?

Question

[Biologist]

I have a list of genes and to get pathways from that I used gProfileR package.

library(gProfileR)
pathways <- gprofiler(genes, organism = "hsapiens", ordered_query = F,
          significant = T, exclude_iea = F, underrep = F, evcodes = F, region_query = F)

The above function gave me list of pathways and saved that results in csv file. Results from gProfileR looks like this gProfileR results

I would like to know how to make a plot out of those results?

[Ram]

Do not paste links to screenshots of tabular data, it's multiple unnecessary layers over something that is far easier to showcase in your post. See

• How to post tabular data
• How to use a Github Gist to post data

[Nitin Narwade]

In this tutorial, they have used web-based g:Profiler for the enrichment analysis and cytoscope for the representation.

It may help you.

Answer 1

[hedi.peterson]

You might want to check the new gprofiler2 package we have at CRAN. This new R package will allow to make the same manhattan plot visualisations as the gprofiler website does.

[Kristoffer Vitting-Seerup]

Interesting! Is there a vignette illustrating gProfileR2's functionality somewhere?

[liis.kolberg]

There is no vignette yet, but getting a first interactive visualisation is as simple as

gostres <- gost(query = c("Klf4", "Pax5", "Sox2", "Nanog"), organism = "mmusculus")
gostplot(gostres)

You can get a static image using gostplot(gostres, interactive = F) Check ?gostplot for more options to customize the plot.

And if you have chosen the functions you want to highlight, then you can generate a good quality image using the following commands:

p <- gostplot(gostres, interactive = FALSE)
publish_gostplot(p, highlight_terms = c("GO:0001010", "WP:WP1763"))

[Ram]

Welcome to Biostars and thank you for the contribution! Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.

[rohitsatyam102]

Here is the link you can learn from. They have created a proper tutorial.