R/plotTFs2Exprs.R

In GianlucaMattei/methyl.O: Annotate, Score and Visualize Differentially Methylated Regions

#' Plot the beta value of TF and related target genes expression
#'
#' Barplot of the beta value of TF and the expression of the target genes
#'
#' @param associatedTFs2Expr data.frame, results from associateTFs2Exprs().
#' @param symbol character, feature to correlate. Must be from names of resulting list from annotateDMRs. Additional feature names can be first exons (exons1) or first intron (intron1). To use more than one feature use c().
#' @param col.meth character, color for beta value. Defaut = "#8e0000" (red)
#' @param pals.bars character, palette for gene expresion. hcl.pals() to show available. Default = "Cold"
#' 
#' @return plot showing methylation levels of TF and expresion of target genes
#'
#' @export


plotTFs2Exprs <- function(associatedTFs2Expr, symbol, col.meth = '#8e0000', pals.bars = 'Cold'){
    cur.slice = associatedTFs2Expr[associatedTFs2Expr$symbol %in% symbol,]
    cur.tf <- cur.slice[1,1]
    cur.bars <- cur.slice['target.expression']
    cur.bars <- rbind(cur.tf,0,cur.bars)
    rownames(cur.bars) <- c(cur.slice[1,2],'',cur.slice[,'target.symbol'])
    marg <- max(abs(c(min(cur.bars) , max(cur.bars))))
    ylimit <- round(marg)
    colors <- c(col.meth, hcl.colors(nrow(cur.bars)-1,pals.bars))
    # colors <- hcl.colors(nrow(cur.bars),pals.bars)
    bords <- rep('black', length(colors))
    bords[2] = 'white'
    barplot(height=cur.bars[,1],names=rownames(cur.bars), las=2, ylim = c(ylimit*-1,ylimit), col = colors, axes=FALSE, border = bords, main = paste0(cur.slice[1,2], ' beta val. and target genes expression'))
    axis(4,at=seq(ylimit*-1,ylimit))
    axis(2,at=seq(-1,1))
}