pagoda2 (version 1.0.12)

view.aspects: Internal function to visualize aspects of transcriptional heterogeneity as a heatmap.

Description

Internal function to visualize aspects of transcriptional heterogeneity as a heatmap.

Usage

view.aspects(
  mat,
  row.clustering = NA,
  cell.clustering = NA,
  zlim = c(-1, 1) * quantile(mat, p = 0.95),
  row.cols = NULL,
  col.cols = NULL,
  cols = colorRampPalette(c("darkgreen", "white", "darkorange"), space = "Lab")(1024),
  show.row.var.colors = TRUE,
  top = Inf,
  ...
)

Value

A heatmap

Arguments

mat

Numeric matrix

row.clustering

Row dendrogram (default=NA)

cell.clustering

Column dendrogram (default=NA)

zlim

numeric Range of the normalized gene expression levels, inputted as a list: c(lower_bound, upper_bound) (default=c(-1, 1)*quantile(mat, p = 0.95)). Values outside this range will be Winsorized. Useful for increasing the contrast of the heatmap visualizations. Default, set to the 5th and 95th percentiles.

row.cols

Matrix of row colors (default=NULL)

col.cols

Matrix of column colors (default=NULL). Useful for visualizing cell annotations such as batch labels.

cols

Heatmap colors (default=colorRampPalette(c("darkgreen", "white", "darkorange"), space = "Lab")(1024))

show.row.var.colors

boolean Whether to show row variance as a color track (default=TRUE)

top

integer Restrict output to the top n aspects of heterogeneity (default=Inf)

...

additional arguments for heatmap plotting