SE-heatmap: Heatmap wrappers for 'SummarizedExperiment-class'.
In SEtools: SEtools: tools for working with SummarizedExperiment

Description Usage Arguments Value Examples

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`	A `SummarizedExperiment-class`.
`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 `getBreaks` function, and indicates the proportion of the points to map to a linear scale, while the more extreme values will be plotted on a quantile scale. 'breaks=FALSE' will disable symmetrical scale and quantile capping, while retaining automatic breaks. 'breaks=1' will produce a symmetrical scale without quantile capping.
`gaps_at`	Columns of 'colData' to use to establish gaps between columns.
`gaps_row`	Passed to `pheatmap`; if missing, will be set automatically according to toporder.
`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').