.plotHeatmap {rliger}

General heatmap plotting with prepared matrix and data.frames

Description

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