plotDistributions: Plot distributions

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

Plot distributions

Description

Plot the distributions of cells across the tissue with overlaying color information. This is a wrapper function for plot

Usage

plotDistributions(
  datIn,
  group,
  groups = NULL,
  colors = rep("black", dim(datIn$mapDat)[2]),
  colormap = gray.colors,
  maxrow = 12,
  pch = 19,
  cex = 1.5,
  xlim = NULL,
  ylim = NULL,
  main = "",
  xlab = "",
  ylab = "",
  ...
)

Arguments

datIn	a fishScaleAndMap output list
group	a character vector (or factor) indicating how to split the data (e.g., cluster call) or a metadata/mappingResults column name
groups	a character vector of groups to show (default is levels of group)
colors	a character vector (or factor) indicating how to color the plots (e.g., layer or gene expression) or a metadata/mappingResults column name (default is all black)
colormap	function to use for the colormap for the data (default gray.colors)
maxrow	maximum number of plots to show in one row (default=12)
pch, cex	for plot. Can be single values or vectors
xlim, ylim	for plot, but will be calculated if not entered
main, xlab, ylab, ...	other parameters for plot (must be single values)

Value

Only returns if there is an error

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