General heatmap plotting with prepared matrix and data.frames

This is not an exported function. This documentation just serves for a manual of extra arguments that users can use when generating heatmaps with plotGeneHeatmap or plotFactorHeatmap.

Note that the following arguments are pre-occupied by upstream wrappers so users should not include them in a function call: dataMatrix, dataName, cellDF, featureDF, cellSplitVar, featureSplitVar.

The following arguments of Heatmap is occupied by this function, so users should include them in a function call as well: matrix, name, col, heatmap_legend_param, top_annotation, column_title_gp, column_names_gp, show_column_names, column_split, column_gap, left_annotation, row_title_gp, row_names_gp, show_row_names, row_split, row_gap.

Usage

.plotHeatmap(
  dataMatrix,
  dataName = "Value",
  cellDF = NULL,
  featureDF = NULL,
  transpose = FALSE,
  cellSplitVar = NULL,
  featureSplitVar = NULL,
  dataScaleFunc = NULL,
  showCellLabel = FALSE,
  showCellLegend = TRUE,
  showFeatureLabel = TRUE,
  showFeatureLegend = TRUE,
  cellAnnColList = NULL,
  featureAnnColList = NULL,
  scale = FALSE,
  trim = c(-2, 2),
  baseSize = 8,
  cellTextSize = NULL,
  featureTextSize = NULL,
  cellTitleSize = NULL,
  featureTitleSize = NULL,
  legendTextSize = NULL,
  legendTitleSize = NULL,
  viridisOption = "A",
  viridisDirection = -1,
  RColorBrewerOption = "RdBu",
  ...
)

Arguments

dataMatrix: Matrix object with features/factors as rows and cells as columns.
dataName: Text for heatmap color bar title. Default Value.
cellDF: data.frame object. Number of rows must match with number of columns of dataMatrix.
featureDF: data.frame object. Number of columns must match with number of rows of dataMatrix.
transpose: Logical, whether to "rotate" the heatmap by 90 degrees so that cell information is displayed by row. Default FALSE.
cellSplitVar, featureSplitVar: Subset columns of cellDF or featureDF, respectively.
dataScaleFunc: A function object, applied to dataMatrix.
showCellLabel, showFeatureLabel: Logical, whether to show cell barcodes, gene symbols or factor names. Default TRUE for gene/factors but FALSE for cells.
showCellLegend, showFeatureLegend: Logical, whether to show cell or feature legends. Default TRUE. Can be a scalar for overall control or a vector matching with each given annotation variable.
cellAnnColList, featureAnnColList: List object, with each element a named vector of R-interpretable color code. The names of the list elements are used for matching the annotation variable names. The names of the colors in the vectors are used for matching the levels of a variable (factor object, categorical). Default NULL generates ggplot-flavor categorical colors.
scale: Logical, whether to take z-score to scale and center gene expression. Applied after dataScaleFunc. Default FALSE.
trim: Numeric vector of two values. Limit the z-score value into this range when scale = TRUE. Default c(-2, 2).
baseSize: One-parameter control of all text sizes. Individual text element sizes can be controlled by other size arguments. "Title" sizes are 2 points larger than "text" sizes when being controlled by this.
cellTextSize, featureTextSize, legendTextSize: Size of cell barcode labels, gene/factor labels, or legend values. Default NULL.
cellTitleSize, featureTitleSize, legendTitleSize: Size of titles of the cell slices, gene/factor slices, or the legends. Default NULL.
viridisOption, viridisDirection: See argument option and direction of viridis. Default "A" and -1.
RColorBrewerOption: When scale = TRUE, heatmap color will be mapped with brewer.pal. This is passed to name. Default "RdBu".
...: Additional arguments to be passed to Heatmap.

Value

HeatmapList-class object