R/Vplot.R

In Rvirgenslane/Hotgenes: For Visualizing Differential Expression Analysis

#' Wrapper for EnhancedVolcano
#' @export
#' @import EnhancedVolcano 
#' @param Hotgenes_input R object generated by DEseq2_export or 
#' Limma_export functions
#' @param pval_cut numeric indicating pvalue cut off
#' @param FCcutoff numeric indicating logfoldchange cut off
#' @param stuffer is a positive number added or subtracted from pvalue 
#' or fold change values, used for x and y limits.
#' @param contrast name or numeric value to retrieve differential 
#' expression data. See names(Hotgenes_input$Output_DE).
#' @examples
#' Example_Hotgenes_dir<-system.file("extdata",
#' "Example_Hotgenes.Rdata",
#' package = "Hotgenes", mustWork = TRUE)
#' load(Example_Hotgenes_dir)
#' names(Example_Hotgenes$Output_DE)
#' Vplot(Example_Hotgenes, contrast = 1)

Vplot<-function(Hotgenes_input=NULL, 
                pval_cut=0.1, 
                FCcutoff=0, 
                stuffer=1,
                contrast=1){
    id_sel<-names(Hotgenes_input$Output_DE[contrast])

    plot_inputff<-Hotgenes_input$Output_DE[[id_sel]]

    if(length(plot_inputff[plot_inputff$pvalue ==0,]$pvalue)>0){
      message("0 pvalue replaced by min(pvalue)")
      temp<-plot_inputff[plot_inputff$pvalue !=0,]
      plot_inputff[plot_inputff$pvalue ==0,]$pvalue<-min(temp$pvalue)
      
    }
    
    
    
    
    xlim_min<-c(min(plot_inputff$log2FoldChange)-stuffer)
    xlim_max<-c(stuffer+max(plot_inputff$log2FoldChange))
    
    ylim_min<-c(min(-log10(plot_inputff$pvalue)-stuffer))
    ylim_max<-c(stuffer+max(-log10(plot_inputff$pvalue)))
    
    sdff<- EnhancedVolcano(plot_inputff,
                           lab = rownames(plot_inputff),
                           x = 'log2FoldChange', y = 'pvalue', 
                           xlim = c( xlim_min,xlim_max), 
                           ylim = c(ylim_min,ylim_max),
                           title = id_sel,
                           pCutoff = pval_cut,
                           FCcutoff = FCcutoff,
                           pointSize =3.0,
                           labSize = 3.0) 
    
    
    return(sdff)}