Plot ADT marker expression density profile with identified peak and valley locations

This function plots the ADT expression density profile with identified peak and valley locations. Each panel is an ADT marker, and each track is a sample. Color by batch

plot_adt_density_with_peak_valley(
  cell_x_adt,
  cell_x_feature,
  adt_marker_select = NULL,
  peak_landmark_list,
  valley_landmark_list,
  brewer_palettes = "Set1",
  parameter_list = NULL
)

Arguments

cell_x_adt

Matrix of ADT raw counts in cells (rows) by ADT markers (columns) format.

cell_x_feature

Matrix of cells (rows) by cell features (columns) such as cell type, sample, and batch-related information.

adt_marker_select

The target ADT marker(s) that the denstiy plot is about. Leave it NULL will generate figures for all the ADT markers available in cell_x_adt.

peak_landmark_list

Matrix of peak landmark locations with rows being samples and columns being the peaks.

valley_landmark_list

Matrix of valley landmark locations with rows being samples and columns being the valleys.

brewer_palettes

Set the color scheme of the color brewer.

parameter_list

Users can specify: "run_label" to give a name for this run; "bw" to adjust the bandwidth of the density plot.

Examples

if (FALSE) {
plot_adt_density_with_peak_valley(
  cell_x_adt,
  cell_x_feature,
  adt_marker_select = c("CD3", "CD4", "CD8", "CD19"),
  peak_landmark_list = peak_mode_norm_res,
  valley_landmark_list = valley_location_norm_res,
  brewer_palettes = "Set1",
  parameter_list = list(bw = 0.1, run_label = "ADTnorm")
)
}