--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/main.R	Fri Mar 12 00:20:13 2021 +0000
@@ -0,0 +1,156 @@
+#!/usr/bin/env Rscript
+
+suppressMessages( library(tidyverse) )
+library( optparse )
+library( naivestates )
+
+## Identify directory of the script
+wd <- commandArgs( trailingOnly=FALSE ) %>%
+    keep( ~grepl("--file=", .x) ) %>%
+    str_replace( "--file=", "" ) %>% dirname()
+cat( "Running the script from", wd, "\n" )
+
+## Parse command-line arugments
+option_list <- list(
+    make_option(c("-i", "--in"), type="character", help="Input file"),
+    make_option(c("-o", "--out"), type="character", default="/data",
+                help="Output directory"),
+    make_option(c("-m", "--markers"), type="character", default="auto",
+                help="Markers to model"),
+    make_option(c("-p", "--plots"), type="character", default="off",
+                help="Generate plots showing the fit"),
+    make_option("--mct", type="character", default="",
+                help="Marker -> cell type map in .csv format"),
+    make_option("--id", type="character", default="CellID",
+                help="Column containing cell IDs"),
+    make_option("--log", type="character", default="auto",
+                help="Whether to apply a log transform <yes|no|auto>"),
+    make_option("--sfx", type="character", default="",
+                help="Common suffix on marker columns (e.g., _cellMask)"),
+    make_option("--umap", action="store_true", default=FALSE,
+                help="Generate UMAP plots")
+)
+opt <- parse_args(OptionParser(option_list=option_list))
+
+## Argument verification
+if( !("in" %in% names(opt)) )
+    stop( "Please provide an input file name with -i" )
+if( !(opt$log %in% c("yes","no","auto")) )
+    stop( "--log must be one of <yes|no|auto>" )
+if( !(opt$plots %in% c("off", "pdf", "png")) )
+    stop( "--plots must be one of <off|pdf|png>" )
+
+## Identify the sample name
+sn <- basename( opt$`in` ) %>% str_split( "\\." ) %>%
+    pluck( 1, 1 )
+cat( "Inferred sample name:", sn, "\n" )
+
+## Read the data matrix
+X <- read_csv( opt$`in`, col_types=cols() )
+cat( "Read", nrow(X), "entries\n" )
+
+## Fix potential capitalization mismatch of --id
+if( !(opt$id %in% colnames(X)) )
+{
+    ## Attempt to find a singular case-insensitive match
+    i <- grep( tolower(opt$id), tolower(colnames(X)) )
+    if( length(i) == 1 )
+    {
+        warning( "  No such column ", opt$id,
+                "; using ", colnames(X)[i], " instead" )
+        opt$id <- colnames(X)[i]
+    }
+    else stop( "No such column ", opt$id,
+              "; use --id to specify which column contains cell IDs" )
+}
+
+## Identify markers in the matrix
+mrkv <- findMarkers(setdiff(colnames(X), opt$id), opt$markers,
+                    opt$sfx, TRUE, TRUE)
+
+## Handle log transformation of the data
+if( opt$log == "yes" ||
+    (opt$log == "auto" && max(X[mrkv], na.rm=TRUE) > 1000) )
+{
+    cat( "Applying a log10 transform\n" )
+    X <- X %>% mutate_at( unname(mrkv), ~log10(.x+1) )
+}
+
+## Fit Gaussian mixture models
+GMM <- GMMfit(X, opt$id, !!!mrkv)
+fnMdl <- file.path( opt$out, str_c(sn, "-models.csv") )
+cat( "Saving models to", fnMdl, "\n" )
+GMMmodels(GMM) %>% write_csv( fnMdl )
+
+## Reshape the matrix back to cells-by-marker format
+Y <- GMMreshape(GMM)
+
+cat( "------\n" )
+
+## Find the default cell type map
+if( opt$mct != "" ) {
+
+    ## Load marker -> cell type associations
+    cat( "Loading cell type map from", opt$mct, "\n" )
+    mct <- read_csv( opt$mct, col_types=cols() ) %>%
+        distinct() %>% filter(Marker %in% colnames(Y))
+
+    if( nrow(mct) == 0 ) {
+        warning( "No usable marker -> cell type mappings detected" )
+        Y <- findDominant(Y, opt$id)
+    } else {
+        cat( "Using the following marker -> cell type map:\n" )
+        walk2( mct$Marker, mct$State, ~cat(.x, "->", .y, "\n") )
+        Y <- callStates(Y, opt$id, mct)
+    }
+} else {
+    cat( "No marker -> cell type mapping provided\n" )
+    Y <- findDominant(Y, opt$id)
+}
+
+cat( "------\n" )
+
+## Identify the output location(s)
+fnOut <- file.path( opt$out, str_c(sn, "-states.csv") )
+cat( "Saving probabilities and calls to", fnOut, "\n")
+Y %>% write_csv( fnOut )
+
+## Generates plots as necessary
+if( opt$plots != "off" )
+{
+    ## Create a separate directory for plots
+    dirPlot <- file.path( opt$out, "plots", sn )
+    dir.create(dirPlot, recursive=TRUE, showWarnings=FALSE)
+
+    ## Fit overview
+    fn <- file.path( file.path(opt$out, "plots"), str_c(sn, "-allfits.", opt$plots) )
+    ggf <- plotFitOverview(GMM)
+    suppressMessages(ggsave( fn, ggf, width=12, height=8 ))
+    
+    ## Compute a UMAP projection
+    if( opt$umap ) {
+        cat( "Computing a UMAP projection...\n" )
+        U <- umap( Y, c(opt$id, "State", "Dominant") )
+    
+        ## Generate and write a summary plot
+        gg <- plotSummary( U )
+        fn <- file.path( file.path(opt$out, "plots"), str_c(sn, "-summary.", opt$plots) )
+        suppressMessages(ggsave( fn, gg, width=9, height=7 ))
+        cat( "Plotted summary to", fn, "\n" )
+
+        ## Generate and write faceted probabilities plot
+        gg <- plotProbs( U, c(opt$id, "State", "Dominant") )
+        fn <- file.path( file.path(opt$out, "plots"), str_c(sn, "-probs.", opt$plots) )
+        suppressMessages(ggsave( fn, gg, width=9, height=7 ))
+        cat( "Plotted probabilities to", fn, "\n" )
+    }
+
+    ## Generate and write out plots for individual marker fits
+    for( i in names(mrkv) )
+    {
+        gg <- plotMarker(GMM, i)
+        fn <- file.path( dirPlot, str_c(i,".",opt$plots) )
+        suppressMessages(ggsave( fn, gg ))
+        cat( "Wrote", fn, "\n" )
+    }
+}