test_starter.R

In caitlinjones/halo: Development version of the package 'halo', which analyzes and visualizes Halo data

library(contoureR)
library(digest)
library(futile.logger)
library(grid)
library(gridExtra)
library(kimisc)
library(magrittr)
library(plotrix)
library(randtoolbox)
library(raster)
library(RColorBrewer)
library(rgeos)
library(rJava)
library(scales)
library(SearchTrees)
library(sp)
library(tidyverse)
library(tools)
library(xlsx)
library(xlsxjars)
library(XML)
library(yaml)

source("/home/byrne/halo/dev/halo/R/melanoma_spatial.R")
source("/home/byrne/halo/dev/halo/R/util.R")
source("/home/byrne/halo/dev/halo/R/spatial_util.R")
source("/home/byrne/halo/dev/halo/R/marker_counts.R")
source("/home/byrne/halo/dev/halo/R/plots.R")

manifest <- "/home/byrne/halo/dev/halo/example/spatial_plots/yaml/PR_manifest.txt"
pp <- initializeProject(manifest)

dataFile = pp$data_file
annotationsDir = pp$annotations_dir
cellTypeFile = pp$cell_types_file
cellTypeName = pp$cell_type_name
fovBB = pp$fov_bb
pad=30
plotBB = pp$plot_bb
pdfFile = 'testing.pdf'
ymax = pp$ymax
log_plot=pp$log_plot
funcMarker = pp$func_marker
sortByMarker = pp$sort_by_marker
sampleColor = pp$sample_color
sampleColorDark = pp$sample_color_dark
exclude_sample_fov = pp$exclude_sample_fov
writeCSVfiles =pp$write_csv_files
haloInfiltrationDir = pp$halo_infiltration_dir
maxG = pp$max_g
outDir = pp$out_dir
byBand = pp$by_band
bandWidth = pp$band_width
maxDistanceFromInterface=pp$max_distance_from_interface