Plot diffusion map colored by other features — plot_diff

Produce a scatter plot where cells are placed according to the results of diffusion map analysis and colored by values given in col_data.

Usage

plot_diff_map(
  scMuffinList = NULL,
  columns = c(1:2),
  col_data = NULL,
  file = NULL,
  width = 200,
  height = 200,
  units = "mm",
  res = 300,
  adj_outliers = TRUE,
  scale_feature = FALSE,
  min_cells = 50,
  ...
)

Arguments

scMuffinList: scMuffinList object
columns: columns of scMuffinList$diffusion_map_pseudo_t$summary to be used for x and y
col_data: named vector with values that will be translated into colors. Names are cell names.
file: File name to save the figure as png file
width: image width
height: image height
units: image units
res: image resolution
adj_outliers: logical, whether to adjust the group.by scores, removing outliers
scale_feature: logical, whether to scale col_data
min_cells: minimum number of cells in which the feature must have a non-zero value
...: further arguments to plot()