ArchRHeatmap: Plot Nice Lookng Heatmap Using Complex Heatmap
In GreenleafLab/ArchR: Analyzing single-cell regulatory chromatin in R.

ArchRHeatmap

R Documentation

Plot Nice Lookng Heatmap Using Complex Heatmap

Description

Plot Nice Lookng Heatmap Using Complex Heatmap

Usage

ArchRHeatmap(
  mat = NULL,
  scale = FALSE,
  limits = c(min(mat), max(mat)),
  colData = NULL,
  color = paletteContinuous(set = "solarExtra", n = 100),
  clusterCols = TRUE,
  clusterRows = FALSE,
  labelCols = FALSE,
  labelRows = FALSE,
  colorMap = NULL,
  useRaster = TRUE,
  rasterQuality = 5,
  split = NULL,
  fontSizeRows = 10,
  fontSizeCols = 10,
  fontSizeLabels = 8,
  colAnnoPerRow = 4,
  showRowDendrogram = FALSE,
  showColDendrogram = FALSE,
  customRowLabel = NULL,
  customRowLabelIDs = NULL,
  customColLabel = NULL,
  customColLabelIDs = NULL,
  customLabelWidth = 0.75,
  rasterDevice = "png",
  padding = 45,
  borderColor = NA,
  draw = TRUE,
  name = "Heatmap"
)

Arguments

`mat`	A matrix to plot heatmap from.
`scale`	A boolean whether to convert to row Z-scores
`limits`	A vector of two values describing min and mix limits to plot
`colData`	A DataFrame matching the columns of the input matrix to overlay on the columns of the heatmap
`color`	A palette to use for heatmap continuous color scheme. See `paletteContinuous`.
`clusterCols`	A boolean describing whether to cluster columns for heatmap.
`clusterRows`	A boolean describing whether to cluster rows for heatmap.
`colorMap`	A list of color mappings matching the column names in colData.
`useRaster`	A boolean whether to use rastering when plotting heatmap.
`rasterQuality`	Raster resolution of raster. Default is set to 5 higher numbers increase resolution.
`split`	A vector of groupings that will split the rows of heatmap (must be equal to nrow(mat)).
`fontSizeRows`	A numeric value representing the font size for rownames.
`fontSizeCols`	A numeric value representing the font size for colnames.
`fontSizeLabels`	A numeric value representing the font size for labels.
`colAnnoPerRow`	An integer value describing the number of column annotations per row in the legend.
`showRowDendrogram`	A boolean whether to show row dendrogram in heatmap.
`showColDendrogram`	A boolean whether to show column dendrogram in heatmap.
`customRowLabel`	A vector of indices to custom label from rows.
`customRowLabelIDs`	A vector of custom labels to overlay. Should match length of `customRowLabel`.
`customColLabel`	A vector of indices to custom label from columns.
`customColLabelIDs`	A vector of custom labels to overlay. Should match length of `customColLabel`.
`customLabelWidth`	A numeric describing the width of the column labels.
`rasterDevice`	Which device to use for rastering see `ComplexHeatmap`.
`padding`	A numeric (in cm) to pad the heatmap ie adding white space so that the final plot doesnt cutoff.
`borderColor`	A character representing the border color for each cell in the heatmap.
`draw`	A boolean whether to draw the heatmap immediately. If FALSE this will return a ComplexHeatmap object.
`name`	A character that will appear above color bar legend in heatmap.