plotMatrix.simple: plot matrix (typically genes expression)
In Japrin/sscVis: simpler single cell RNAseq data Visualization

plotMatrix.simple

R Documentation

plot matrix (typically genes expression)

Description

plot matrix (typically genes expression)

Usage

plotMatrix.simple(
  dat,
  out.prefix = NULL,
  mytitle = "Heatmap",
  show.number = NULL,
  gp.show.number = gpar(),
  my.cell_fun = NULL,
  do.clust = NULL,
  z.lo = NULL,
  z.hi = NULL,
  z.len = 100,
  palatte = NULL,
  clust.row = FALSE,
  clust.column = FALSE,
  show.dendrogram = FALSE,
  waterfall.row = FALSE,
  waterfall.column = FALSE,
  row.ann.dat = NULL,
  row.split = NULL,
  column.split = NULL,
  returnHT = FALSE,
  par.legend = list(),
  par.heatmap = list(),
  col.ht = NULL,
  col.ann = NULL,
  top_annotation = NULL,
  par.warterfall = list(score.alpha = 1.5, do.norm = T),
  fig.func = pdf,
  par.fig = list(),
  pdf.width = 8,
  pdf.height = 8,
  exp.name = "Count",
  ...
)

Arguments

`dat`	matrix; matrix
`out.prefix`	character; output prefix.
`mytitle`	character; (default: "Heatmap")
`show.number`	logical; (default: NULL)
`gp.show.number`	object of gpar; (default: gpar() )
`my.cell_fun`	function; cell_fun of Heatmap (default: NULL )
`do.clust`	logical, character or dendrogram; passed to both cluster_columns and cluster_rows of Heatmap. Higher priority than clust.row and clust.column (default: NULL)
`z.lo`	double; (default: NULL)
`z.hi`	double; (default: NULL)
`z.len`	integer; (default: 100)
`palatte`	character; (default: NULL)
`clust.row`	logical, character or dendrogram; passed to cluster_rows of Heatmap (default: FALSE)
`clust.column`	logical, character or dendrogram; passed to cluster_columns of Heatmap (default: FALSE)
`show.dendrogram`	logical, whetehr show the dendrogram (default: FALSE)
`waterfall.row`	logical, order rows to make plot like waterfall (default: FALSE)
`waterfall.column`	logical, order rows to make plot like waterfall (default: FALSE)
`row.ann.dat`	data.frame; data for row annotation; rownames(row.ann.dat) cannot be NULL; (default: NULL)
`row.split`	vector; used for row; (default: NULL)
`column.split`	vector; used for column; (default: NULL)
`returnHT`	logical; whether return HT; (default: FALSE)
`par.legend`	list; lengend parameters, used to overwrite the default setting; (default: list())
`par.heatmap`	list; other heatmap parameters, (default: list())
`col.ht`	vector; (default: NULL)
`col.ann`	list; (default: NULL)
`top_annotation`	passed to Heatmap; (default: NULL)
`par.warterfall`	list; parameters for warterfall, sucah as score.alpha
`pdf.width`	double; width of the output plot (default: 22)
`pdf.height`	double; height of the output plot (default: 22)
`exp.name`	character; showd in the legend (default: "Count")
`...`	parameters passed to ComplexHeatmap::draw
`fig.type`	character; type of output file (default: "pdf")