crossHm {SEtools} | R Documentation |
These functions have been moved and will be deprecated from this package; please use the [sechm](https://bioconductor.org/packages/release/bioc/html/sechm.html) package instead.
crossHm( ses, genes, do.scale = TRUE, uniqueScale = FALSE, assayName = .getDef("assayName"), sortBy = seq_along(ses), only.common = TRUE, cluster_cols = FALSE, cluster_rows = is.null(sortBy), toporder = NULL, hmcols = NULL, breaks = .getDef("breaks"), gaps_at = .getDef("gaps_at"), gaps_row = NULL, anno_rows = .getDef("anno_rows"), anno_columns = .getDef("anno_columns"), name = NULL, anno_colors = list(), show_rownames = NULL, merge_legends = FALSE, show_colnames = FALSE, rel.width = NULL, ... )
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). |
uniqueScale |
Logical; whether to force the same colorscale for each heatmap. |
assayName |
The name of the assay to use; if multiple names are given, the first available will be used. Defaults to "logcpm", "lognorm". |
sortBy |
Names or indexes of 'ses' to use for sorting rows (default all) |
only.common |
Logical; whether to plot only rows common to all SEs (default TRUE). |
cluster_cols |
Logical; whether to cluster columns (default FALSE). |
cluster_rows |
Logical; whether to cluster rows (default TRUE if 'do.sortRows=FALSE', FALSE otherwise). |
toporder |
Optional verctor of categories on which to supra-order when sorting rows, or name of a 'rowData' column to use for this purpose. |
hmcols |
Colors for the heatmap. |
breaks |
Breaks for the heatmap colors. Alternatively, symmetrical
breaks can be generated automatically by setting 'breaks' to a numerical
value between 0 and 1. The value is passed as the 'split.prop' argument to
the |
gaps_at |
Columns of 'colData' to use to establish gaps between columns. |
gaps_row |
A named vector according to which rows will be split. |
anno_rows |
Columns of 'rowData' to use for annotation. |
anno_columns |
Columns of 'colData' to use for annotation. |
name |
The title of the heatmap key. |
anno_colors |
List of colors to use for annotation. |
show_rownames |
Whether to show row names (default TRUE if 50 rows or less). |
merge_legends |
Logical; passed to
|
show_colnames |
Whether to show column names (default FALSE). |
rel.width |
Relative width of the heatmaps |
... |
Any other parameter passed to each call of
|
Plot a multi-panel heatmap from a list of
SummarizedExperiment-class
.
A Heatmap list.
data("SE", package="SEtools") se1 <- SE[,1:10] se2 <- SE[,11:20] se3 <- mergeSEs( list(se1=se1, se2=se2) )