Plot heatmap

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

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