Make a Heatmap of Aggregated Gene Expressionf from a CDS

Supply a cds subset and aggregation values and get a heatmap. Plot the return value using cowplot::plot_grid(). This function wraps several complicated functions from ComplexHeatmap and tries to apply default values for the most common use case: plotting top markers from a cds with cells grouped arbitrarily (usually by cluster of some type). This function provides the option to aggregate by genes as well in order to plot gene modules. For cell and gene aggregation, provide a name (in the form of a string) of the corresponding metadata column and the aggregation will be performed. There are many aesthetic parameters for this function and even more available for the internal ComplexHeatmap::Heatmap() function. The best way to adjust parameters not provided here is to scroll the popup box that appears when you type ComplexHeatmap::Heatmap() in RStudio and pass them in via the ellipsis. The default is to put genes in columns and cells in rows. You can flip this behavior by setting flip_axis = TRUE. This will require adjustment of some aesthetic parameters. Complex annotations (beyond labeling cherry-picked genes) are not currently supported.

Usage

bb_cds_heatmap(
  cds_subset,
  cellmeta_col = NULL,
  rowmeta_col = NULL,
  heatmap_highlights = NULL,
  three_colors = c("blue4", "ivory", "red3"),
  flip_axis = FALSE,
  name = NULL,
  heatmap_legend_param = list(title_gp = gpar(fontface = "plain", fontsize = 9),
    grid_width = unit(0.14, "in"), labels_gp = gpar(fontsize = 8)),
  row_dend_width = unit(5, "mm"),
  column_dend_height = unit(5, "mm"),
  column_dend_side = "bottom",
  show_row_names = T,
  row_names_gp = gpar(fontsize = 9),
  show_column_names = F,
  row_dend_gp = gpar(lwd = 0.5),
  column_dend_gp = gpar(lwd = 0.5),
  row_title = NULL,
  column_title = NULL,
  padding = 1.5,
  labels_rot = 45,
  ...
)

Arguments

cds_subset: The subset of cells and genes you want to plot as a heatmap. Best approach is to pipe the cds through filter_cds() and into this function.
cellmeta_col: The name of a cell metadata column to aggregate cells by; one of cellmeta_col and rowmeta_col must not be NULL, Default: NULL
rowmeta_col: The name of a row metadata column to aggregate cells by; one of cellmeta_col and rowmeta_col must not be NULL, Default: NULL
heatmap_highlights: A vector of gene names to highlight using anno_mark(), Default: NULL
three_colors: A vector of colors for the main color scale, Default: c("blue4", "ivory", "red3")
flip_axis: Logical; whether to plot genes as rows (TRUE) or columns (FALSE), Default: FALSE
name: Name of the main color scale, Default: NULL
heatmap_legend_param: Graphical parameters for the main heatmap legend, Default: list(title_gp = gpar(fontface = "plain", fontsize = 9), grid_width = unit(0.14, "in"), labels_gp = gpar(fontsize = 8))
row_dend_width: Row dendrogram width, Default: unit(5, "mm")
column_dend_height: Column dendrogram height, Default: unit(5, "mm")
column_dend_side: Side on which to plot the column dendrogram, Default: 'bottom'
show_row_names: Logical; whether or not to show rownames, Default: T
row_names_gp: Graphical parameters for the row names, Default: gpar(fontsize = 9)
show_column_names: Logical; whether or not to show column names, Default: F
row_dend_gp: Graphical parameters for the row dendrogram, Default: gpar(lwd = 0.5)
column_dend_gp: Graphical parameters for teh column dendrogram, Default: gpar(lwd = 0.5)
row_title: Row title text, Default: NULL
column_title: Column title text, Default: NULL
padding: Padding between gene names on the heatmap highlights, Default: 1.5
labels_rot: Rotation of the heatmap highlight labels, Default: 45
...: Optional arguments to pass to ComplexHeatmap::Heatmap()

Value

A complex heatmap in the form of a gtree.