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?
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written
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Biologist
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.
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hedi.peterson •
Interesting! Is there a vignette illustrating gProfileR2's functionality somewhere?
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"))
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Here is the link you can learn from. They have created a proper tutorial.
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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
In this tutorial, they have used web-based g:Profiler for the enrichment analysis and cytoscope for the representation.
It may help you.