LINCS Report

In MetaIntegrator: Meta-Analysis of Gene Expression Data

Drugs

load(params$rdataFilePath)
library(pheatmap)
library(knitr)
###################################################
###Function 3, lincsHeatmap
###################################################
lincsHeatmap = function(hit.expression, cutoff = as.numeric(params$cutoff), 
                                                pert.ordered = as.logical(params$pert.ordered),
                                                gene.ordered = as.logical(params$gene.ordered), 
                                                transpose = as.logical(params$transpose),
                                                scale = as.logical(params$scale), 
                                                resize = as.logical(params$resize), hm.title = NULL, out.file = NULL
                                                ,cluster_rows = F,cluster_cols= T){

    hit.expression = hit.expression[order(hit.expression$sig),]

    ###Apply cutoff... useful for getting the data to be 0 centered
    if(!is.null(cutoff)){
        hit.expression[hit.expression > cutoff] = cutoff
        hit.expression[hit.expression < -cutoff] = -cutoff
    }


    ###Scale if desired
    if(scale) hit.expression = scale(hit.expression)

    ##Order from most to least correlated to the signature
    if(pert.ordered){
        cor.order = t(cor(hit.expression[,"sig"],hit.expression))
        cor.order = cor.order[order(-cor.order[,1]),,drop=F]
        hit.expression = hit.expression[,rownames(cor.order)]
    }

    ###Transpose if desired
    if(transpose) hit.expression = as.data.frame(t(hit.expression))

    hm.command = "heatmap = pheatmap(hit.expression
    ,clustering_method = 'ward.D2',clustering_distance_cols = 'manhattan'
    ,clustering_distance_rows = 'manhattan'
    ,color =colorRampPalette(c('navy', 'white', 'firebrick3'))(50)"
    if(resize)hm.command = paste(hm.command,"
                                                             ,cellwidth = 10, cellheight = 10",sep="")
    if(!is.null(hm.title))hm.command = paste(hm.command,"
                                                                                     ,main = hm.title",sep="")
    if(!is.null(out.file)) hm.command = paste(hm.command,"
                                                                                        ,filename = '",out.file,"'",sep="")

    hm.command = paste(hm.command,"
                                         ,cluster_rows =cluster_rows, cluster_cols =cluster_cols)",sep="")

    eval(parse(text = hm.command))

}

lincsHeatmap(cp.conn.rev$hit.expression, hm.title = "Top Reversing Drugs")
DT::datatable(cp.conn.rev.hits)

lincsHeatmap(cp.conn.agg$hit.expression, hm.title = "Top Aggravating Drugs")
DT::datatable(cp.conn.agg.hits)

shRNAs

lincsHeatmap(sh.conn.rev$hit.expression, hm.title = "Top Reversing shRNAs (Possible Targets for Reversing the Signature)")
DT::datatable(sh.conn.rev.hits)

lincsHeatmap(sh.conn.agg$hit.expression,hm.title = "Top Aggravating shRNAs (Possible Targets for Aggravating the Signature")
DT::datatable(sh.conn.agg.hits)

Over Expressions

lincsHeatmap(oe.conn.rev$hit.expression, hm.title = "Top Reversing OverExpressions")
DT::datatable(oe.conn.rev.hits)

lincsHeatmap(oe.conn.agg$hit.expression, hm.title = "Top Aggravating OverExpressions")
DT::datatable(oe.conn.agg.hits)

Ligands

lincsHeatmap(lig.conn.rev$hit.expression, hm.title = "Top Reversing Ligands (Possible mAB Targets for Aggravating the Signature)")
DT::datatable(lig.conn.rev.hits)

lincsHeatmap(lig.conn.agg$hit.expression, hm.title = "Top Aggravating Ligands (Possible mAB Targets for Reversing the Signature")
DT::datatable(lig.conn.agg.hits)

Mutations

lincsHeatmap(mut.conn.rev$hit.expression, hm.title = "Top Reversing Mutations (Possible Reversal Pathways)")
DT::datatable(mut.conn.rev.hits)

lincsHeatmap(mut.conn.agg$hit.expression, hm.title = "Top Aggravating Mutations (Possible Drivers or Driver Pathways)")
DT::datatable(mut.conn.agg.hits)

MetaIntegrator documentation built on March 26, 2020, 6:29 p.m.