archive/show_comparsion_of_modules.R

In Sage-Bionetworks/AMPAD:

synapser::synLogin()
foobar <- synapser::synTableQuery("select * from syn11932957")$asDataFrame()
foobar <- foobar[,-c(1,2)]
load('aggregateNonAdModules.rda')

AggregateModuleManifest <- rbind(dlpfc_mods$df,
                                 cbe_mods$df,
                                 tcx_mods$df,
                                 ifg_mods$df,
                                 stg_mods$df,
                                 phg_mods$df,
                                 fp_mods$df)

mod1=c(paste0('all',unique(AggregateModuleManifest$Module)),paste0('ad',unique(foobar$Module)))
annrow <- data.frame(moduleType=c(rep('All',length(unique(AggregateModuleManifest$Module))),
                                  rep('AD',length(unique(foobar$Module)))),
                     stringsAsFactors=F)
rownames(annrow) <- mod1


mats <- utilityFunctions::pairwiseMatrixOfEnrichments(key=c(paste0('all',AggregateModuleManifest$Module),paste0('ad',foobar$Module)),
                                                      value=c(AggregateModuleManifest$GeneID,foobar$GeneID))
pheatmap::pheatmap(-log10(mats$pval+1e-300),annotation_row=annrow)


tiff(filename='adnonadoverlap.tiff',height=85,width=85,units='mm',res=300)
pheatmap::pheatmap(-log10(mats$pval+1e-300),
                   show_colnames = F,
                   border_color = NA,
                   fontsize=3,
                   treeheight_row=10,
                   treeheight_col=10,
                   annotation_col=annrow)
dev.off()