Plot heatmap of using data stored in SingleCellExperiment Object

plotSCEHeatmap(
  inSCE,
  useAssay = "logcounts",
  doLog = FALSE,
  featureIndex = NULL,
  cellIndex = NULL,
  scale = TRUE,
  trim = c(-2, 2),
  featureIndexBy = "rownames",
  cellIndexBy = "rownames",
  rowDataName = NULL,
  colDataName = NULL,
  featureAnnotations = NULL,
  cellAnnotations = NULL,
  featureAnnotationColor = NULL,
  cellAnnotationColor = NULL,
  rowSplitBy = NULL,
  colSplitBy = NULL,
  rowLabel = FALSE,
  colLabel = FALSE,
  rowLabelSize = 8,
  colLabelSize = 8,
  rowDend = TRUE,
  colDend = TRUE,
  title = NULL,
  rowTitle = "Genes",
  colTitle = "Cells",
  rowGap = grid::unit(0, "mm"),
  colGap = grid::unit(0, "mm"),
  border = FALSE,
  colorScheme = NULL,
  ...
)

plotSCEDimReduceHeatmap(
  inSCE,
  useReducedDim,
  featureIndex = NULL,
  cellIndex = NULL,
  doLog = FALSE,
  scale = FALSE,
  trim = c(-2, 2),
  cellIndexBy = "rownames",
  colDataName = NULL,
  featureAnnotations = NULL,
  cellAnnotations = NULL,
  featureAnnotationColor = NULL,
  cellAnnotationColor = NULL,
  rowSplitBy = NULL,
  colSplitBy = NULL,
  rowLabel = FALSE,
  colLabel = FALSE,
  rowLabelSize = 8,
  colLabelSize = 8,
  rowDend = TRUE,
  colDend = TRUE,
  title = NULL,
  rowTitle = "Dimensions",
  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. Only for plotSCEHeatmap.
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.
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)
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. Not applicable for plotSCEDimReduceHeatmap. 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".
rowDataName: character. The column name(s) in rowData that need to be added to the annotation. Not applicable for plotSCEDimReduceHeatmap. Default NULL.
colDataName: character. The column name(s) in colData that need to be added to the annotation. Default NULL.
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.
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.
rowLabelSize: A number for the font size of feature names. Default 8
colLabelSize: A number for the font size of cell names. Default 8
rowDend: Whether to display row dendrogram. Default TRUE.
colDend: Whether to display column dendrogram. Default TRUE.
title: The main title of the whole plot. Default NULL.
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.
useReducedDim: character. A string indicating the reducedDim name that provides the expression level to plot. Only for plotSCEDimReduceHeatmap.

Value

A ggplot object.

Author

Yichen Wang

Examples

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