plot_immunoflo: Generate plot of TMA point process

In spatialTIME: Spatial Analysis of Vectra Immunoflourescent Data

Generate plot of TMA point process

Description

This function generates plot of point process in rectangular or circular window.

Usage

plot_immunoflo(
  mif,
  plot_title,
  mnames,
  mcolors = NULL,
  cell_type = NULL,
  filename = NULL,
  path = NULL
)

Arguments

mif	MIF object created using create_MIF().
plot_title	Character string or vector of character strings of variable name(s) to serve as plot title(s).
mnames	Character vector containing marker names.
mcolors	Character vector of color names to display markers in the plot.
cell_type	Character vector of cell type
filename	Character string of file name to store plots. Plots are generated as single .pdf file.
path	Different path than file name or to use in conjunction with filename ???

Value

mif object and the ggplot objects can be viewed form the derived slot of the mif object

Examples

#Create mif object
library(dplyr)
x <- create_mif(clinical_data = example_clinical %>% 
mutate(deidentified_id = as.character(deidentified_id)),
sample_data = example_summary %>% 
mutate(deidentified_id = as.character(deidentified_id)),
spatial_list = example_spatial,
patient_id = "deidentified_id", 
sample_id = "deidentified_sample")

mnames_good <- c("CD3..Opal.570..Positive","CD8..Opal.520..Positive",
"FOXP3..Opal.620..Positive","PDL1..Opal.540..Positive",
"PD1..Opal.650..Positive","CD3..CD8.","CD3..FOXP3.")

x <- plot_immunoflo(x, plot_title = "deidentified_sample", mnames = mnames_good, 
cell_type = "Classifier.Label")

x[["derived"]][["spatial_plots"]][[4]]

spatialTIME documentation built on April 1, 2023, 12:18 a.m.