moduleHeatmap: Heatmap for featureModules

moduleHeatmapR Documentation

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.