heatmap.contrasts — heatmap.contrasts • DEprot

Plots an heatmap of the log2(FoldChange) for differentially expressed proteins

heatmap.contrasts(
  DEprot.analyses.object,
  contrasts = NULL,
  top.n = NULL,
  distance.method = "euclidean",
  clustering.method = "complete",
  high.color = "firebrick",
  low.color = "#2166AC",
  mid.color = "white",
  na.color = "gray",
  cell.border.color = NA,
  cell.border.width = 0.5,
  title = NULL,
  show.protein.names = FALSE,
  use.uncorrected.pvalue = FALSE
)

Arguments

DEprot.analyses.object: An object of class DEprot.analyses.
contrasts: Numeric vector indicating the position of the contrast to use for the plotting. Default: NULL (all contrasts).
top.n: Numeric value indicated the top differentially expressed proteins to consider for each contrast selected. The rank is based on the product of log2Fc and -log10Padj. Default: NULL (all differential proteins).
distance.method: The distance measure to be used. This must be one of "euclidean", "maximum", "manhattan", "canberra", "binary" or "minkowski". Any unambiguous substring can be given. Default: "euclidean".
clustering.method: The agglomeration method to be used. This should be (an unambiguous abbreviation of) one of "ward.D", "ward.D2", "single", "complete", "average" (= UPGMA), "mcquitty" (= WPGMA), "median" (= WPGMC) or "centroid" (= UPGMC). Default: complete"}.}\item{high.color}{String indicating the color to use for up-regulated protein FoldChanges in the plot. Default: \code{"indianred"}.}\item{low.color}{String indicating the color to use for down-regulated protein FoldChanges in the plot. Default: \code{"#2166AC" (blue).
mid.color: String indicating the color to use for the 0 in the plots. Default: "white".
na.color: String indicating the color to use for the NA values in the heatmap. Default: "gray".
cell.border.color: String indicating the color to use for the individual cells border. Default: NA (no border).
cell.border.width: Numeric value indicating the width of the cell border line. Ignored when cell.border.color = NA. Default: 0.5.
title: String indicating the title to use, markdown formatting supported. Default: NULL (automatic title).
show.protein.names: Logical value to indicate whether the protein names should be displayed. Default: FALSE.
use.uncorrected.pvalue: Logical value indicating whether it should be used the normal p-value instead of the adjusted one (differential proteins numbers are recomputed). Default: FALSE, padj is used.

Value

A DEprot.contrast.heatmap object, which contains the heatmap (ggplot) and the hclust object used to order the rows.