crossHm {SEtools} | R Documentation |
Plot a multi-panel heatmap from a list of
SummarizedExperiment-class
crossHm(ses, genes, do.scale = TRUE, uniqueColorScale = FALSE, assayName = .getDef("assayName"), do.sortRows = TRUE, only.common = TRUE, anno_columns = .getDef("anno_columns"), spreadAnnotation = FALSE, hmcols = NULL, cluster_columns = FALSE, cluster_rows = !do.sortRows, show_rownames = ifelse(length(genes) < 80, "once", FALSE), show_colnames = FALSE, anno_colors = .getDef("anno_colors"), ...)
ses |
A (named) list of
|
genes |
A vector of genes/row.names to plot. |
do.scale |
Logical; whether to scale rows in each SE (default TRUE). |
uniqueColorScale |
Logical; whether to force the same colorscale for each heatmap (default FALSE; applicable only when what!='asis'). |
assayName |
The name of the assay to use; if multiple names are given, the first available will be used. Defaults to "logcpm", "lognorm". |
do.sortRows |
Logical; whether to sort rows according to MDS (default TRUE). |
only.common |
Logical; whether to plot only rows common to all SEs (default TRUE). |
anno_columns |
A vector of colData columns to use (if available) for annotation, default "Condition" and "TimePoint". |
spreadAnnotation |
Logical; whether to spread annotation to all SEs (not yet supported) |
hmcols |
An optional color palette, such as produced by the 'colorRampPalette' function. |
cluster_columns |
Logical; whether to cluster columns (default FALSE). |
cluster_rows |
Logical; whether to cluster rows (default TRUE if 'do.sortRows=FALSE', FALSE otherwise). |
show_rownames |
Logical; whether to show row names (default TRUE if 'length(genes)<80', FALSE otherwise). |
show_colnames |
Logical; whether to show column names (default FALSE) |
anno_colors |
A vector of color for annotations. |
... |
Any other parameter passed to each call of
|
A Heatmap-class
object.
data("SE", package="SEtools") crossHm(list(se1=SE[,1:10], se2=SE[,11:20]), head(row.names(SE)))