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Question: How to make a plot with gProfileR results?
0
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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?

ADD COMMENTlink 16 months ago Biologist • 150 • updated 10 months ago hedi.peterson • 20
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0

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

ADD REPLYlink 16 months ago
RamRS
21k
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0

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

It may help you.

ADD REPLYlink 16 months ago
Nitin Narwade
• 400
2
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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.

ADD COMMENTlink 10 months ago hedi.peterson • 20 • updated 10 months ago RamRS 21k
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Interesting! Is there a vignette illustrating gProfileR2's functionality somewhere?

ADD REPLYlink 10 months ago
kristoffer.vittingseerup
♦ 1.8k
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0

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"))
ADD REPLYlink 10 months ago
liis.kolberg
• 0
• updated 10 months ago
RamRS
21k
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0

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.
code_formatting

ADD REPLYlink 10 months ago
RamRS
21k

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