DDheatmap: DDHeatmap

In lyc-1995/DoubletDeconSeurat: Seurat wrappers with DoubletDecon

Description

This function is a modified version of heatmap.2 from the gplots package (https://cran.r-project.org/package=gplots), corrected by ChristophH (https://github.com/ChristophH/gplots/blob/master/R/heatmap.2.R) to correct the issue of dendrogram generation even with row and column clustering off and dendrogram set to "none".

Usage

DDheatmap(
  x,
  Rowv = TRUE,
  Colv = if (symm) "Rowv" else TRUE,
  distfun = dist,
  hclustfun = hclust,
  dendrogram = c("both", "row", "column", "none"),
  reorderfun = function(d, w) reorder(d, w),
  symm = FALSE,
  scale = c("none", "row", "column"),
  na.rm = TRUE,
  revC = identical(Colv, "Rowv"),
  add.expr,
  breaks,
  symbreaks = any(x < 0, na.rm = TRUE) || scale != "none",
  col = "heat.colors",
  colsep,
  rowsep,
  sepcolor = "white",
  sepwidth = c(0.05, 0.05),
  cellnote,
  notecex = 1,
  notecol = "cyan",
  na.color = par("bg"),
  trace = c("column", "row", "both", "none"),
  tracecol = "cyan",
  hline = median(breaks),
  vline = median(breaks),
  linecol = tracecol,
  margins = c(5, 5),
  ColSideColors,
  RowSideColors,
  cexRow = 0.2 + 1/log10(nr),
  cexCol = 0.2 + 1/log10(nc),
  labRow = NULL,
  labCol = NULL,
  srtRow = NULL,
  srtCol = NULL,
  adjRow = c(0, NA),
  adjCol = c(NA, 0),
  offsetRow = 0.5,
  offsetCol = 0.5,
  colRow = NULL,
  colCol = NULL,
  key = TRUE,
  keysize = 1.5,
  density.info = c("histogram", "density", "none"),
  denscol = tracecol,
  symkey = any(x < 0, na.rm = TRUE) || symbreaks,
  densadj = 0.25,
  key.title = NULL,
  key.xlab = NULL,
  key.ylab = NULL,
  key.xtickfun = NULL,
  key.ytickfun = NULL,
  key.par = list(),
  main = NULL,
  xlab = NULL,
  ylab = NULL,
  lmat = NULL,
  lhei = NULL,
  lwid = NULL,
  extrafun = NULL,
  ...
)

lyc-1995/DoubletDeconSeurat documentation built on March 8, 2020, 5:47 a.m.