--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/contamination_plot.R	Thu Jan 24 09:52:58 2019 -0500
@@ -0,0 +1,140 @@
+#!/usr/bin/env R
+
+require(ggplot2)
+
+log10histoPlot <- function(columncounts, title=""){
+    #' Log10 histogram plot
+    #'
+    #' @param columncounts colSums(input_matrix)
+    #' @param title Title of plot
+    #' @return ggplot grob
+    dfer <- data.frame(colcounts=log10(columncounts))
+    p1 <- ggplot(dfer, aes(x=colcounts)) +
+        geom_histogram(binwidth = 0.05, color="black",fill="white") +
+        theme(plot.title = element_text(hjust = 0.5)) +
+        labs(title=title, y="Frequency", x="Library Size (Log10)")
+
+    return(p1)
+}
+
+contaminationPlot <- function(columncounts, title = "",
+                              indexes.plates, indexes.fullbc, indexes.truebc,
+                              filtered=FALSE)
+{
+    #' Plots true and false barcodes
+    #'
+    #'
+    #' @param columncounts colSums(input_matrix)
+    #' @param title plot title
+    #' @param indexes.plates plate line positions
+    #' @param indexes.fullbc full batch line positions
+    #' @param indexes.truebc true batch line positions
+    #' @param filtered specifies whether the positions have been adjusted for true barcodes
+    #' @return ggplot grob
+    dfer <- data.frame(colcounts=columncounts)
+
+    ## Remove indexes where plates and full barcodes mix
+    indexes.fullbc = indexes.fullbc[!(indexes.fullbc %in% indexes.plates)]
+    
+    nit <- length(indexes.truebc)
+    nif <- length(indexes.fullbc)
+    nip <- length(indexes.plates)
+    mval <- max(dfer)
+  
+    ## Aesthetics
+    min.height <- -200
+    tf.spacing.left <- 12
+    tf.spacing.right <- 12   
+    tf.height <- mval - 10000
+    bn.height <- mval - 2000
+    plate.color <- "grey"
+    plate.text.color <- "black"
+    plate.text.alpha <- 0.5
+    plate.text.size <- 3
+    plate.height <- 2* mval / 5
+    plate.spacing <- if (filtered) 12 else 24
+    plate.height.text <- plate.height - 3000
+    
+    truebcs <- data.frame(
+        x=indexes.truebc, y=rep(min.height,nit),
+        xend=indexes.truebc, yend=rep(mval,nit)
+    )
+    fullbcs <- data.frame(
+        x=indexes.fullbc, y=rep(min.height,nif),
+        xend=indexes.fullbc, yend=rep(mval,nif)
+    )
+    platess <- data.frame(
+        x=indexes.plates, y=rep(min.height,nip),
+        xend=indexes.plates, yend=rep(plate.height,nip)
+    )
+    connecting.bar <- data.frame(
+        xsta = min(indexes.plates), ysta = min.height,
+        xfin = max(indexes.plates), yfin = min.height
+    )
+      
+    p1 <- ggplot()
+
+    if (!filtered){
+        p1 <- p1 +
+            geom_segment(data=truebcs, aes(x=x,y=y,xend=xend,yend=yend - 4000), col='grey', lty=2, size=0.2) + 
+            geom_segment(data=fullbcs, aes(x=x,y=y,xend=xend,yend=yend), col='blue', lty=1, size=0.4, alpha=0.2)
+    }
+    else {
+        p1 <- p1 +
+            geom_segment(data=truebcs, aes(x=x,y=y,xend=xend,yend=yend), col='blue', lty=1, size=0.4, alpha=0.2)
+    }
+    
+    p1 <- p1 +
+        geom_segment(data=platess, aes(x=x,y=y,xend=xend,yend=yend), col=plate.color, lty=1, size=1) +
+        geom_segment(data=connecting.bar, aes(x=xsta,y=ysta,xend=xfin,yend=yfin), col=plate.color, lty=1, size=1) +
+        geom_point(
+            data=dfer, aes(x=1:length(rownames(dfer)), y=dfer$colcounts),
+            pch = 16, cex = 1) +
+        theme(plot.title = element_text(hjust = 0.5),
+              axis.ticks.x=element_blank(), axis.ticks.y=element_blank(),
+              axis.text.x=element_blank()) +
+        labs(title=paste("Contamination Plot\n", title), y="Library Size", x="Barcode Index") +
+        scale_y_continuous(breaks=seq(0,mval + 10000, 10000)) +
+        scale_x_continuous(breaks=NULL)
+
+    ## Add true/false and batch labels
+    res <- lapply(indexes.truebc, function(xval){
+        batch <- match(xval, indexes.truebc)
+
+        if (!filtered){
+            p1 <<- p1 +
+                annotate("text", x=xval - tf.spacing.left, size=2, y=tf.height, angle=90, label=" true positives", color = "dark blue", alpha = 0.5) +
+                annotate("text", x=xval + tf.spacing.right, size=2, y=tf.height, angle=-90,label="false positives", color = "black", alpha = 0.5) +
+                annotate("text", x=xval , size=4, y=bn.height, angle=-90, label=paste("B",batch,sep=""), color = "grey", alpha = 0.8)
+        }
+        else {
+            p1 <<- p1 +
+                annotate("text", x=xval - 48, size=4, y=bn.height, angle=-90, label=paste("B",batch,sep=""), color = "grey", alpha = 0.8)
+        }
+    })
+
+    ## Add Plate labels
+    res <- lapply(indexes.plates, function(p){
+        plate.num <- match(p, indexes.plates)
+        c.label <- paste("Plate", plate.num, sep="")
+        b.label <- paste("Plate", plate.num - 1, sep="")
+
+        # Right label
+        if (plate.num <  length(indexes.plates)){
+            p1 <<- p1 +
+                annotate("text", x=p + plate.spacing, size=plate.text.size, y=plate.height.text, angle=-90,
+                         label=c.label, color = plate.text.color, alpha=plate.text.alpha)
+        }
+
+        # Left label
+        if (plate.num > 1){
+            p1 <<- p1 +
+                annotate("text", x=p - plate.spacing, size=plate.text.size, y=plate.height.text, angle=90,
+                         label=b.label, color = plate.text.color,  alpha=plate.text.alpha)
+        }
+    })
+        
+    return(p1)
+}
+
+