PlotExpProb: PlotExpProb

In plevritis-lab/CELESTA: Cell type identification with spatial information

PlotExpProb

Description

Plots the expression probabilities of cells in the tissue

Usage

PlotExpProb(
  coords,
  marker_exp_prob,
  prior_marker_info,
  size_to_use = 1,
  width_to_use = 5,
  height_to_use = 4,
  save_plot = TRUE,
  output_dir = "."
)

Arguments

coords	the x, y coordinates of each cell
marker_exp_prob	the marker expression probability for each cell
prior_marker_info	user-defined cell-type signature matrix. The data should contain two columns (name X and Y) for the x, y coordinates and a column for each protein marker. Each row represents the data for a single cell, including its x, y coordinates and expression for each protein marker.
size_to_use	the size of the points in the plot
width_to_use	the width of the plot
height_to_use	the height of the plot
save_plot	whether to save the plot
output_dir	the path to the directory to where the plot will be outputted. This defaults to the directory containing CELESTA_functions.R. Note that the directory must exist.

Value

writes a plot of the expression probabilities for each marker

plevritis-lab/CELESTA documentation built on Jan. 30, 2023, 3:32 p.m.