view.aspects: View heatmap

In scde: Single Cell Differential Expression

Description

Internal function to visualize aspects of transcriptional heterogeneity as a heatmap. Used by pagoda.view.aspects.

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, ...)

Arguments

mat	Numeric matrix
row.clustering	Row dendrogram
cell.clustering	Column dendrogram
zlim	Range of the normalized gene expression levels, inputted as a list: c(lower_bound, upper_bound). 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.
col.cols	Matrix of column colors. Useful for visualizing cell annotations such as batch labels.
cols	Heatmap colors
show.row.var.colors	Boolean of whether to show row variance as a color track
top	Restrict output to the top n aspects of heterogeneity
...	additional arguments for heatmap plotting

Value

A heatmap

scde documentation built on Nov. 8, 2020, 6:19 p.m.