plotSCEHeatmap {singleCellTK} | R Documentation |
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, ... )
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 |
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 |
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 |
A single character specifying a column name of
|
cellIndexBy |
A single character specifying a column name of
|
featureAnnotations |
|
cellAnnotations |
|
featureAnnotationColor |
A named list. Customized color settings for
feature labeling. Should match the entries in the |
cellAnnotationColor |
A named list. Customized color settings for
cell labeling. Should match the entries in the |
rowDataName |
character. The column name(s) in |
colDataName |
character. The column name(s) in |
rowSplitBy |
character. Do semi-heatmap based on the grouping of
this(these) annotation(s). Should exist in either |
colSplitBy |
character. Do semi-heatmap based on the grouping of
this(these) annotation(s). Should exist in either |
rowLabel |
Use a logical for whether to display all the feature names,
a single character to display a column of |
colLabel |
Use a logical for whether to display all the cell names, a
single character to display a column of |
rowDend |
Whether to display row dendrogram. Default |
colDend |
Whether to display column dendrogram. Default |
scale |
Whether to perform z-score scaling on each row. Default
|
trim |
A 2-element numeric vector. Values outside of this range will be
trimmed to their nearst bound. Default |
title |
The main title of the whole plot. Default |
rowTitle |
The subtitle for the rows. Default |
colTitle |
The subtitle for the columns. Default |
rowGap |
A numeric value or a |
colGap |
A numeric value or a |
border |
A logical scalar. Whether to show the border of the heatmap or
splitted heatmaps. Default |
colorScheme |
function. A function that generates color code by giving
a value. Can be generated by |
... |
Other arguments passed to |
A Heatmap
object
Yichen Wang
data(scExample, package = "singleCellTK") plotSCEHeatmap(sce[1:3,1:3], useAssay = "counts")