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

This function plots the ADT expression density profile with identified peak and valley locations for only one ADT marker. Each track is a sample. Color by batch

plot_adt_density_with_peak_valley_each(
  adt_count,
  cell_x_feature,
  peak_landmark_list,
  valley_landmark_list,
  brewer_palettes = "Set1",
  parameter_list = NULL
)

Arguments

adt_count

Matrix of ADT raw counts in cells (rows) by one target ADT marker (column) format.

cell_x_feature

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

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_each(
  cell_x_adt,
  cell_x_feature,
  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")
)
}