archive/spatial_plots.R

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

#!/home/byrne/R/R-3.4.3/bin/R

options( java.parameters = c("-Xss2560k", "-Xmx8g") )
options('python_cmd'='/opt/common/CentOS_6-dev/python/python-3.5.1/bin/python')

write("Loading libraries...",stdout())
suppressPackageStartupMessages(library("argparse"))
#suppressPackageStartupMessages(library("halo"))
suppressPackageStartupMessages(library("halodev"))

###
# Parse user input
###
parser <- ArgumentParser()
## args are preferrably all in manifest
parser$add_argument("-m", "--manifest", type="character", default=NULL, 
                    help="file containing all project parameters; run ?initializeProject for details")
parser$add_argument("--cellTypeLocations", action="store_true", default=FALSE, 
                    help="plot cell type locations for each sample FOV")
parser$add_argument("--plotDensity", action="store_true", default=FALSE, 
                    help="plot total density of cells within a set distance from a tumor boundary")
parser$add_argument("--debug", action="store_true", default=FALSE, 
                    help="print extra output for debugging")

args <- parser$parse_args()
####################################################

usage <- function(){
    stop("Usage: Rscript spatial_plots.R -m manifest.txt")
}

pp <- NULL

## eventually set up defaults for everything, then allow everything to be
## passed on command line; for now require manifest
print(args$manifest)
if(!is.null(args$manifest)){
    pp <- initializeProject(args$manifest,type="spatial_plots")
    flog.info("Pulled params from manifest %s",args$manifest)
} else {
    usage()
}

if(!is.null(pp)){
    logParams(pp,"Making spatial plots")
}

if(args$cellTypeLocations){
    flog.info("Plotting cell type locations")
    pdfFile <- gsub("\\.rda","_cellTypeLocations.pdf",basename(pp$data_file))
    plotCellTypeLocations(pp$data_file, pp$annotations_dir, pp$cell_types_file, pp$fov_bb, pp$plot_bb,
                          pp$boundary_colors, pp$cell_type_colors, pad=pp$pad, pdfFile=pdfFile)
}

#stop()

if(args$plotDensity){
    flog.info("Plotting total density")

    plotDensity(pp$data_files, 
                pp$annotations_dirs, 
                pp$marker_set_files, 
                pp$cell_type_name, 
                pp$pad, 
                pp$pdf_file, 
                densityFiles=pp$density_files,
                logPlot=pp$log_plot,
                funcMarker=pp$func_marker, 
                funcPosColor=pp$functional_pos_color, 
                funcNegColor=pp$functional_neg_color,
                sampleColor=pp$sample_color, 
                sampleColorDark=pp$sample_color_dark, 
                exclude_sample_fov=pp$exclude_sample_fov, 
                sortByMarker=pp$sort_by_marker, 
                sampleOrder=pp$sample_order,
                outDir=pp$out_dir,
                writeCSVfiles=pp$write_csv_files, 
                maxG=pp$max_g,
                byBand=pp$by_band,
                bandWidth=pp$band_width, 
                maxDistanceFromInterface=pp$max_distance_from_interface,
                plotPer=pp$plot_per,
                filePer=pp$file_per,
                includeSortByMarker=pp$include_sort_by_marker,
                consistentYScaling=pp$consistent_y_scaling,
                boxPlots=pp$box_plots)
}