sechm {sechm} | R Documentation |
ComplexHeatmap wrapper for
SummarizedExperiment-class
.
sechm( se, genes, do.scale = FALSE, assayName = .getDef("assayName"), name = NULL, 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, left_annotation = .getDef("anno_rows"), right_annotation = NULL, top_annotation = .getDef("anno_columns"), bottom_annotation = NULL, anno_rows = NULL, anno_columns = NULL, anno_colors = list(), show_rownames = NULL, show_colnames = FALSE, isMult = FALSE, show_heatmap_legend = !isMult, show_annotation_legend = TRUE, mark = NULL, na_col = "white", annorow_title_side = ifelse(show_colnames, "bottom", "top"), includeMissing = FALSE, sort.method = "MDS_angle", ... )
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. |
name |
The name of the heatmap, eventually appearing as title of the color scale. |
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 the heatmap function; if missing, will be set automatically according to toporder. |
left_annotation |
Columns of 'rowData' to use for left annotation. Alternatively, an 'HeatmapAnnotation' object. |
right_annotation |
Columns of 'rowData' to use for left annotation. Alternatively, an 'HeatmapAnnotation' object. |
top_annotation |
Columns of 'colData' to use for top annotation. Alternatively, an 'HeatmapAnnotation' object. |
bottom_annotation |
Columns of 'colData' to use for bottom annotation. Alternatively, an 'HeatmapAnnotation' object. |
anno_rows |
Deprecated. Use 'left_annotation' or 'right_annotation' instead. |
anno_columns |
Deprecated. Use 'top_annotation' or 'bottom_annotation' instead. |
anno_colors |
List of colors to use for annotation. |
show_rownames |
Whether to show row names (default TRUE if less than 50 rows to plot). |
show_colnames |
Whether to show column names (default FALSE). |
isMult |
Logical; used to silence labels when plotting multiple heatmaps |
show_heatmap_legend |
Logical; whether to show heatmap legend |
show_annotation_legend |
Logical; whether to show the annotation legend. |
mark |
An optional vector of gene names to highlight. |
na_col |
Color of NA values |
annorow_title_side |
Side (top or bottom) of row annotation names |
includeMissing |
Logical; whether to include missing genes (default FALSE) |
sort.method |
Row sorting method (see |
... |
Further arguments passed to 'Heatmap' |
A a Heatmap-class
.
data("Chen2017", package="sechm") sechm(Chen2017, row.names(Chen2017)[1:10], do.scale=TRUE)