Add node colors to a CellGraph — color_by

Adds node colors based on the expression of a single or multiple markers. If multiple markers are provided, their values are either multiplied or summed depending on the mode.

Usage

color_by_marker(
  cg,
  markers,
  smooth_counts = TRUE,
  palette = "viridis",
  rev_pal = FALSE,
  mode = c("product", "sum"),
  normalize = TRUE,
  trim_quantiles = c(0, 1),
  nNodes = NULL
)

Arguments

cg: A CellGraph object
markers: A character vector with valid marker IDs
smooth_counts: Applies neighborhood smoothing of marker counts. Each node marker counts is combined with the sum of marker counts in a neighborhood of length 1.
palette: A valid color palette from RColorBrewer or viridis or a vector of colors.
rev_pal: Should the palette be reversed?
mode: Only used if more than 1 marker is provided. With mode = "product", the marker counts are multiplied and with mode = "sum", the marker counts are summed. This step is executed after smoothing.
normalize: Apply normalization to the marker counts after smoothing and the multiplication/summation step. The values are first divided by the node degree followed by log-transformation with log1p.
trim_quantiles: A numeric vector of length 2 specifying quantiles to trim. This can be useful to reduce the influence of outliers. The specified quantiles are calculated from the marker counts values prior to normalization. (see section below for details)
nNodes: Number of nodes to keep in the graph

Trim quantile

Sometimes, a few outliers can dominate which makes the colors difficult to interpret. With trim_quantiles, we can remove such outliers. By setting the upper bound to 0.99, we are calculating the 99th quantile of the marker count values and any values above this threshold are replaced with the value for the 99th quantile. The same thing applies to the lower bound but the other way around.