spatialTIME (version 1.3.4-4)

plot_immunoflo: 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,
  xloc = NULL,
  yloc = NULL
)

Value

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

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 ???

xloc, yloc

columns in the spatial files containing the x and y locations of cells. Default is `NULL` which will result in `xloc` and `yloc` being calculated from `XMin`/`YMin` and `XMax`/`YMax`

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]]