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egeulgen / pathfindR

pathfindR: Enrichment Analysis Utilizing Active Subnetworks
https://egeulgen.github.io/pathfindR/
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bubble chart #20

Closed csantosrocha closed 5 years ago

csantosrocha commented 5 years ago

Hi. I'm wondering if we can specify the number or pathways (e.g Top10) to be displayed in the bubble charts

YunielFM commented 5 years ago

Hi, I had the same thought, but solved it by getting the resulting object from the pathfindr analysis and customizing it using ggplot2 (filter, shading, coloring).

YunielFM commented 5 years ago

Just to be a bit more specific, the result from the pathfindR is a dataframe that you can save internally in R, with the following columns: ID, Pathway, Fold_Enrichment, occurrence, lowest_p, highest_p, Up_regulated, Down_regulated. You can decide to filter your top10 genes according to some of them (Panther uses the pvalue, but you can chose here also the pathway enrichment as a criterion.). After filtering you will only need to do an easy plot using ggplot2 or your favourite library from the CRAN.

egeulgen commented 5 years ago

hey @csantosrocha, there is no argument for selecting top X pathways but you can subset the resulting data frame of run_pathfindR and use the subset as the input for enrichment_chart, the function for creating the bubble chart