Plot heatmap of using data stored in SingleCellExperiment Object

plotSCEHeatmap(
  inSCE,
  useAssay = "logcounts",
  doLog = FALSE,
  featureIndex = NULL,
  cellIndex = NULL,
  featureIndexBy = "rownames",
  cellIndexBy = "rownames",
  featureAnnotations = NULL,
  cellAnnotations = NULL,
  featureAnnotationColor = NULL,
  cellAnnotationColor = NULL,
  rowDataName = NULL,
  colDataName = NULL,
  rowSplitBy = NULL,
  colSplitBy = NULL,
  rowLabel = FALSE,
  colLabel = FALSE,
  rowDend = TRUE,
  colDend = TRUE,
  scale = TRUE,
  trim = c(-2, 2),
  title = "SCE Heatmap",
  rowTitle = "Genes",
  colTitle = "Cells",
  rowGap = grid::unit(0, "mm"),
  colGap = grid::unit(0, "mm"),
  border = FALSE,
  colorScheme = NULL,
  ...
)

Arguments

inSCE	SingleCellExperiment inherited object.
useAssay	character. A string indicating the assay name that provides the expression level to plot.
doLog	Logical scalar. Whether to do `log(assay + 1)` transformation on the assay indicated by `useAssay`. Default `FALSE`.
featureIndex	A vector that can subset the input SCE object by rows (features). Alternatively, it can be a vector identifying features in another feature list indicated by `featureIndexBy`. Default `NULL`.
cellIndex	A vector that can subset the input SCE object by columns (cells). Alternatively, it can be a vector identifying cells in another cell list indicated by `featureIndexBy`. Default `NULL`.
featureIndexBy	A single character specifying a column name of `rowData(inSCE)`, or a vector of the same length as `nrow(inSCE)`, where we search for the non-rowname feature indices. Default `"rownames"`.
cellIndexBy	A single character specifying a column name of `colData(inSCE)`, or a vector of the same length as `ncol(inSCE)`, where we search for the non-rowname cell indices. Default `"rownames"`.
featureAnnotations	`data.frame`, with `rownames` containing all the features going to be plotted. Character columns should be factors. Default `NULL`.
cellAnnotations	`data.frame`, with `rownames` containing all the cells going to be plotted. Character columns should be factors. Default `NULL`.
featureAnnotationColor	A named list. Customized color settings for feature labeling. Should match the entries in the `featureAnnotations` or `rowDataName`. For each entry, there should be a list/vector of colors named with categories. Default `NULL`.
cellAnnotationColor	A named list. Customized color settings for cell labeling. Should match the entries in the `cellAnnotations` or `colDataName`. For each entry, there should be a list/vector of colors named with categories. Default `NULL`.
rowDataName	character. The column name(s) in `rowData` that need to be added to the annotation. Default `NULL`.
colDataName	character. The column name(s) in `colData` that need to be added to the annotation. Default `NULL`.
rowSplitBy	character. Do semi-heatmap based on the grouping of this(these) annotation(s). Should exist in either `rowDataName` or `names(featureAnnotations)`. Default `NULL`.
colSplitBy	character. Do semi-heatmap based on the grouping of this(these) annotation(s). Should exist in either `colDataName` or `names(cellAnnotations)`. Default `NULL`.
rowLabel	Use a logical for whether to display all the feature names, a single character to display a column of `rowData(inSCE)` annotation, a vector of the same length as full/subset `nrow(inSCE)` to display customized info. Default `FALSE`.
colLabel	Use a logical for whether to display all the cell names, a single character to display a column of `colData(inSCE)` annotation, a vector of the same length as full/subset `ncol(inSCE)` to display customized info. Default `FALSE`.
rowDend	Whether to display row dendrogram. Default `TRUE`.
colDend	Whether to display column dendrogram. Default `TRUE`.
scale	Whether to perform z-score scaling on each row. Default `TRUE`.
trim	A 2-element numeric vector. Values outside of this range will be trimmed to their nearst bound. Default `c(-2, 2)`
title	The main title of the whole plot. Default `"SCE Heatmap"`
rowTitle	The subtitle for the rows. Default `"Genes"`.
colTitle	The subtitle for the columns. Default `"Cells"`.
rowGap	A numeric value or a `unit` object. For the gap size between rows of the splitted heatmap. Default `grid::unit(0, 'mm')`.
colGap	A numeric value or a `unit` object. For the gap size between columns of the splitted heatmap. Default `grid::unit(0, 'mm')`.
border	A logical scalar. Whether to show the border of the heatmap or splitted heatmaps. Default `TRUE`.
colorScheme	function. A function that generates color code by giving a value. Can be generated by `colorRamp2`. Default `NULL`.
...	Other arguments passed to `Heatmap`.

Value

A Heatmap object

Author

Yichen Wang

Examples

data(scExample, package = "singleCellTK")
plotSCEHeatmap(sce[1:3,1:3], useAssay = "counts")