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Sage-Bionetworks / NF_LandscapePaper_2019

This repository hosts all the code used to generate analyses and figures for the landscape paper
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Updated metaviper/gsea enrichment #92

Closed allaway closed 4 years ago

allaway commented 4 years ago

By drug, this time. This is more interesting than the previous one, but based on the network plots it's pretty clear that this analysis effectively disregards any drugs with only a few listed targets. I included all drugs, though, but pretty much all of the highest-enriched drugs are have a broad range of protein targets

allaway commented 4 years ago

Whoops, didn't realize it was in the wrong directory. just fixed that!

sgosline commented 4 years ago

Re-cap of offline conversation: I think it'd be helpful to include bargraph of number of targets for each drug alongside the enrichment plots

Additional question - is the foldchange in the network actually correlation? If so this is interesting.

allaway commented 4 years ago

the latest version of this pr has this code:


tab <- lapply(names(res_complt), function(x){
  foo <- res_complt[[x]]@result %>%
    mutate(latent_var = x) %>%
    select(latent_var, everything())
}) %>% bind_rows()

# lv_drug_tab <- synBuildTable("Latent Variable Drug Set Enrichment
Analysis", "syn21046734", tab)
# synStore(lv_drug_tab)

DT::datatable(tab)

pushed to this table: https://www.synapse.org/#!Synapse:syn21442304/tables/

On Mon, Dec 16, 2019 at 2:18 PM Sara JC Gosline notifications@github.com wrote:

@sgosline requested changes on this pull request.

In 30-viper-drug-enrichment-bydrug.Rmd https://github.com/Sage-Bionetworks/NF_LandscapePaper_2019/pull/92#discussion_r358495907 :

+}, mc.cores = parallel::detectCores()) + +names(res) <- tidy$latent_var + +##determine if no results for a given LV +empty_idx <- lapply(res, function(x){

  • if(nrow(x@result)==0){
  • TRUE
  • }else{
  • FALSE
  • } +})

  • +##remove if no results +res_complt <- res[empty_idx==F]

Can you post a table of the the drug x LV enrichment scores and p-values to Synapse? I'd like to pull it down in the correlation analysis.

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allaway commented 4 years ago

Re-cap of offline conversation: I think it'd be helpful to include bargraph of number of targets for each drug alongside the enrichment plots

Additional question - is the foldchange in the network actually correlation? If so this is interesting.

@sgosline barplots are added in the latest version of this branch!