Description Usage Arguments Value Author(s) Examples
View source: R/plotSCEHeatmap.R
Plot heatmap of using data stored in SingleCellExperiment Object
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 | 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
1 2 | data(scExample, package = "singleCellTK")
plotSCEHeatmap(sce[1:3,1:3], useAssay = "counts")
|
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