R/diffPlot.R

In kordastilab/ImmunoCluster: Fast and accesible Immune profiling CyTOF data

#' @export
diffPlot <- function(
  pval_df,
  p_val = "padj",
  threshold = 0.1
){

  # Function deprecated
  .Deprecated("volcanoPlot")

  # Extract plot data
  plotdf <- data.frame(logfc = pval_df$logfc, pvalue = pval_df[,p_val], cluster = pval_df$cluster)

  # Remove INF rows
  plotdf <- plotdf[!is.infinite(plotdf$logfc),]

  # Create volcano plot
  gg_logFC = ggplot(plotdf, aes(x=logfc, y=-log(pvalue))) +
    geom_point(aes(color=(-log(pvalue)>-log(threshold)), size=1)) +
    theme_bw() +
    scale_color_manual(values = c('grey', 'red2')) +
    geom_label_repel(data = plotdf,
                     aes(x=logfc, y=-log(pvalue),
                         label = ifelse(-log(pvalue) > -log(threshold),
                                        as.character(cluster) ,"")), point.padding = 2, force = 10) +
    xlab("LogFC") + ylab("-log(FDR)") + theme(legend.position = "none")

  return(gg_logFC)

}