plotHeatmap: Plot heatmap

In AllenInstitute/mfishtools: Building Gene Sets and Mapping mFISH Data

Plot heatmap

Description

Plot the heatmap of cells ordering by a specified order. This is a wrapper for heatmap.2

Usage

plotHeatmap(
  datIn,
  group,
  groups = NULL,
  grouplab = "Grouping",
  useScaled = FALSE,
  capValue = Inf,
  colormap = grey.colors(1000),
  pch = 19,
  xlim = NULL,
  ylim = NULL,
  Rowv = FALSE,
  Colv = FALSE,
  dendrogram = "none",
  trace = "none",
  margins = c(6, 10),
  rowsep = NULL,
  sepwidth = c(0.4, 0.4),
  key = FALSE,
  ...
)

Arguments

datIn	a fishScaleAndMap output list
group	a character vector (or factor) indicating how to order the heatmap (e.g., cluster call) or a metadata/mappingResults column name
groups	a character vector of groups to show (default is levels of group)
grouplab	label for the grouping in the heatmap (default is 'Grouping' or the value for group)
useScaled	plot the scaled (TRUE) or unscaled (FALSE; default) values
capValue	values above capValue will be capped at capValue (default is none)
colormap	set of values to use for the colormap for the data (default heat_colors)
Rowv, Colv, dendrogram, trace, margins, rowsep, colsep, key, ...	other parameters for heatmap.2 (some default values are different)

Value

Only returns if there is an error

AllenInstitute/mfishtools documentation built on July 5, 2023, 4:20 p.m.