SE-heatmap {SEtools} | R Documentation |
SummarizedExperiment-class
.Heatmap wrappers for
SummarizedExperiment-class
.
sechm( se, genes, do.scale = FALSE, assayName = .getDef("assayName"), sortRowsOn = seq_len(ncol(se)), cluster_cols = FALSE, cluster_rows = is.null(sortRowsOn), 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, show_colnames = FALSE, isMult = FALSE, show_heatmap_legend = !isMult, includeMissing = FALSE, ... ) sehm( se, genes, do.scale = FALSE, assayName = .getDef("assayName"), sortRowsOn = seq_len(ncol(se)), cluster_cols = FALSE, cluster_rows = is.null(sortRowsOn), 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"), anno_colors = .getAnnoCols(se), show_rownames = NULL, show_colnames = FALSE, ... )
se |
|
genes |
An optional vector of genes (i.e. row names of 'se') |
do.scale |
Logical; whether to scale rows (default FALSE). |
assayName |
An optional vector of assayNames to use. The first available will be used, or the first assay if NULL. |
sortRowsOn |
Sort rows by MDS polar order using the specified columns (default all) |
cluster_cols |
Whether to cluster columns (default F) |
cluster_rows |
Whether to cluster rows; default FALSE if 'do.sortRows=TRUE'. |
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 |
Passed to |
anno_rows |
Columns of 'rowData' to use for annotation. |
anno_columns |
Columns of 'colData' to use for annotation. |
name |
The name of the heatmap, eventually appearing as title of the color scale. |
anno_colors |
List of colors to use for annotation. |
show_rownames |
Whether to show row names (default TRUE if 50 rows or less). |
show_colnames |
Whether to show column names (default FALSE). |
isMult |
Logical; used to silence labels when plotting mulitple heatmaps |
show_heatmap_legend |
Logical; whether to show heatmap legend |
includeMissing |
Logical; whether to include missing genes (default FALSE) |
... |
Further arguments passed to 'pheatmap' ('sehm') or 'Heatmap' ('sechm'). |
A heatmap (see pheatmap
), or, for 'sechm',
a Heatmap-class
.
data("SE", package="SEtools") sehm(SE, row.names(SE)[1:10], do.scale=TRUE)