moduleHeatmap: Heatmap for featureModules

In campbio/celda: CEllular Latent Dirichlet Allocation

Heatmap for featureModules

Description

Renders a heatmap for selected featureModule. Cells are ordered from those with the lowest probability of the module on the left to the highest probability on the right. Features are ordered from those with the highest probability in the module on the top to the lowest probability on the bottom.

Usage

moduleHeatmap(
  x,
  useAssay = "counts",
  altExpName = "featureSubset",
  modules = NULL,
  featureModule = NULL,
  col = circlize::colorRamp2(c(-2, 0, 2), c("#1E90FF", "#FFFFFF", "#CD2626")),
  topCells = 100,
  topFeatures = NULL,
  normalizedCounts = NA,
  normalize = "proportion",
  transformationFun = sqrt,
  scaleRow = scale,
  showFeatureNames = TRUE,
  displayName = NULL,
  trim = c(-2, 2),
  rowFontSize = NULL,
  showHeatmapLegend = FALSE,
  showTopAnnotationLegend = FALSE,
  showTopAnnotationName = FALSE,
  topAnnotationHeight = 5,
  showModuleLabel = TRUE,
  moduleLabel = "auto",
  moduleLabelSize = NULL,
  byrow = TRUE,
  top = NA,
  unit = "mm",
  ncol = NULL,
  useRaster = TRUE,
  returnAsList = FALSE,
  ...
)

## S4 method for signature 'SingleCellExperiment'
moduleHeatmap(
  x,
  useAssay = "counts",
  altExpName = "featureSubset",
  modules = NULL,
  featureModule = NULL,
  col = circlize::colorRamp2(c(-2, 0, 2), c("#1E90FF", "#FFFFFF", "#CD2626")),
  topCells = 100,
  topFeatures = NULL,
  normalizedCounts = NA,
  normalize = "proportion",
  transformationFun = sqrt,
  scaleRow = scale,
  showFeatureNames = TRUE,
  displayName = NULL,
  trim = c(-2, 2),
  rowFontSize = NULL,
  showHeatmapLegend = FALSE,
  showTopAnnotationLegend = FALSE,
  showTopAnnotationName = FALSE,
  topAnnotationHeight = 5,
  showModuleLabel = TRUE,
  moduleLabel = "auto",
  moduleLabelSize = NULL,
  byrow = TRUE,
  top = NA,
  unit = "mm",
  ncol = NULL,
  useRaster = TRUE,
  returnAsList = FALSE,
  ...
)

Arguments

x	A numeric matrix of counts or a SingleCellExperiment with the matrix located in the assay slot under useAssay. Rows represent features and columns represent cells. Celda results must be present under metadata(altExp(x, altExpName)).
useAssay	A string specifying which assay slot to use if x is a SingleCellExperiment object. Default "counts".
altExpName	The name for the altExp slot to use. Default "featureSubset".
modules	Integer Vector. The featureModule(s) to display. Multiple modules can be included in a vector. Default NULL which plots all module heatmaps.
featureModule	Same as modules. Either can be used to specify the modules to display.
col	Passed to Heatmap. Set color boundaries and colors.
topCells	Integer. Number of cells with the highest and lowest probabilities for each module to include in the heatmap. For example, if topCells = 50, the 50 cells with the lowest probabilities and the 50 cells with the highest probabilities for each featureModule will be included. If NULL, all cells will be plotted. Default 100.
topFeatures	Integer. Plot 'topFeatures' features with the highest probabilities in the module heatmap for each featureModule. If NULL, plot all features in the module. Default NULL.
normalizedCounts	Integer matrix. Rows represent features and columns represent cells. If you have a normalized matrix result from normalizeCounts, you can pass through the result here to skip the normalization step in this function. Make sure the colnames and rownames match the object in x. This matrix should correspond to one generated from this count matrix assay(altExp(x, altExpName), i = useAssay). If NA, normalization will be carried out in the following form normalizeCounts(assay(altExp(x, altExpName), i = useAssay), normalize = "proportion", transformationFun = sqrt). Use of this parameter is particularly useful for plotting many module heatmaps, where normalizing the counts matrix repeatedly would be too time consuming. Default NA.
normalize	Character. Passed to normalizeCounts if normalizedCounts is NA. Divides counts by the library sizes for each cell. One of 'proportion', 'cpm', 'median', or 'mean'. 'proportion' uses the total counts for each cell as the library size. 'cpm' divides the library size of each cell by one million to produce counts per million. 'median' divides the library size of each cell by the median library size across all cells. 'mean' divides the library size of each cell by the mean library size across all cells. Default "proportion".
transformationFun	Function. Passed to normalizeCounts if normalizedCounts is NA. Applies a transformation such as sqrt, log, log2, log10, or log1p. If NULL, no transformation will be applied. Occurs after normalization. Default sqrt.
scaleRow	Function. Which function to use to scale each individual row. Set to NULL to disable. Occurs after normalization and log transformation. For example, scale will Z-score transform each row. Default scale.
showFeatureNames	Logical. Whether feature names should be displayed. Default TRUE.
displayName	Character. The column name of rowData(altExp(x, altExpName)) that specifies the display names for the features. Default NULL, which displays the row names. Only works if showFeaturenames is TRUE and x is a SingleCellExperiment object.
trim	Numeric vector. Vector of length two that specifies the lower and upper bounds for plotting the data. This threshold is applied after row scaling. Set to NULL to disable. Default c(-2,2).
rowFontSize	Numeric. Font size for feature names. If NULL, then the size will automatically be determined. Default NULL.
showHeatmapLegend	Passed to Heatmap. Show legend for expression levels.
showTopAnnotationLegend	Passed to HeatmapAnnotation. Show legend for cell annotation.
showTopAnnotationName	Passed to HeatmapAnnotation. Show heatmap top annotation name.
topAnnotationHeight	Passed to HeatmapAnnotation. Column annotation height. rowAnnotation. Show legend for module annotation.
showModuleLabel	Show left side module labels.
moduleLabel	The left side row titles for module heatmap. Must be vector of the same length as featureModule. Default "auto", which automatically pulls module labels from x.
moduleLabelSize	Passed to gpar. The size of text (in points).
byrow	Passed to matrix. logical. If FALSE (the default) the figure panel is filled by columns, otherwise the figure panel is filled by rows.
top	Passed to marrangeGrob. The title for each page.
unit	Passed to unit. Single character object defining the unit of all dimensions defined.
ncol	Integer. Number of columns of module heatmaps. If NULL, then this will be automatically calculated so that the number of columns and rows will be approximately the same. Default NULL.
useRaster	Boolean. Rasterizing will make the heatmap a single object and reduced the memory of the plot and the size of a file. If NULL, then rasterization will be automatically determined by the underlying Heatmap function. Default TRUE.
returnAsList	Boolean. If TRUE, then a list of plots will be returned instead of a single multi-panel figure. These plots can be displayed using the grid.draw function. Default FALSE.
...	Additional parameters passed to Heatmap.

Value

A list object if plotting more than one module heatmaps. Otherwise a HeatmapList object is returned.

Examples

data(sceCeldaCG)
moduleHeatmap(sceCeldaCG, displayName = "rownames")

campbio/celda documentation built on April 5, 2024, 11:47 a.m.