plotSCEHeatmap: Plot heatmap of using data stored in SingleCellExperiment...

Description Usage Arguments Value Author(s) Examples

View source: R/plotSCEHeatmap.R

Description

Plot heatmap of using data stored in SingleCellExperiment Object

Usage

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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(s)

Yichen Wang

Examples

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

singleCellTK documentation built on Nov. 8, 2020, 5:21 p.m.