--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Dotplot_Release/R_dotPlot.R	Fri Jan 29 09:56:02 2016 -0500
@@ -0,0 +1,83 @@
+#!/usr/bin/env Rscript
+
+args <- commandArgs(trailingOnly = TRUE)
+
+library('latticeExtra')
+library('colorRamps')
+
+data.file <- read.table("SC_data.txt", sep="\t", header=TRUE, row.names=1) ### import spectral count data
+data.file2 <- read.table("FDR_data.txt", sep="\t", header=TRUE, row.names=1) ### import FDR count data
+data.file3 <- read.table("clustered_matrix.txt", sep="\t", header=TRUE, row.names=1) ### import clustered matrix
+data.file4 <- scan("singletons.txt", what="", sep="\n", strip.white=T) ### import singleton data
+
+#setting parameters
+
+Sfirst=as.numeric(args[1]) #first FDR cutoff
+Ssecond=as.numeric(args[2]) #second FDR cutoff
+maxp=as.integer(args[3]) #maximum value for a spectral count
+
+#calculate column and row lengths
+
+#determine bait and prey ordering
+
+bait_levels=names(data.file3)
+prey_levels=c(rownames(data.file3),data.file4)
+
+x_ord=factor(row.names(data.file),levels=prey_levels)
+y_ord=factor(names(data.file),levels=bait_levels)
+
+df<-data.frame(y=rep(y_ord,nrow(data.file))
+	,x=rep(x_ord, each=ncol(data.file))
+	,z1=as.vector(t(data.file)) # Circle color
+	,z2=as.vector(t(data.file/apply(data.file,1,max))) # Circle size
+	,z3=as.vector(t(data.file2)) # FDR
+)
+	
+df$z1[df$z1>maxp] <- maxp #maximum value for spectral count
+df$z2[df$z2==0] <- NA
+df$z3[df$z3>Ssecond] <- 0.05*maxp
+df$z3[df$z3<=Ssecond & df$z3>Sfirst] <- 0.5*maxp
+df$z3[df$z3<=Sfirst] <- 1*maxp
+df$z4 <- df$z1
+df$z4[df$z4==0] <- 0
+df$z4[df$z4>0] <- 2.5 
+
+# The labeling for the colorkey
+
+labelat = c(0, maxp)
+labeltext = c(0, maxp)
+
+# color scheme to use
+
+nmb.colors<-maxp
+z.colors<-grey(rev(seq(0,0.9,0.9/nmb.colors))) #grayscale color scale
+
+#plot
+
+pl <- levelplot(z1~x*y, data=df
+	,col.regions =z.colors #terrain.colors(100)
+	,scales = list(x = list(rot = 90), y=list(cex=0.8), tck=0) # rotates X,Y labels and changes scale 
+	,colorkey = FALSE
+	,xlab="Prey", ylab="Bait"
+	,panel=function(x,y,z,...,col.regions){
+		print(x)
+		z.c<-df$z1[ (df$x %in% as.character(x)) & (df$y %in% y)]
+		z.2<-df$z2[ (df$x %in% as.character(x)) & (df$y %in% y)]
+		z.3<-df$z3
+		z.4<-df$z4
+		panel.xyplot(x,y
+			,as.table=TRUE
+			,pch=21 # point type to use (circles in this case)
+			,cex=((z.2-min(z.2,na.rm=TRUE))/(max(z.2,na.rm=TRUE)-min(z.2,na.rm=TRUE)))*3 #circle size
+			,fill=z.colors[floor((z.c-min(z.c,na.rm=TRUE))*nmb.colors/(max(z.c,na.rm=TRUE)-min(z.c,na.rm=TRUE)))+1] # circle colors
+			,col=z.colors[1+z.3] # border colors
+			,lex=z.4 #border thickness
+			)
+	}
+	#,main="Fold change" # graph main title
+	)
+if(ncol(data.file) > 4) ht=3.5+(0.36*((ncol(data.file)-1)-4)) else ht=3.5
+if(nrow(data.file) > 20) wd=8.25+(0.29*(nrow(data.file)-20)) else wd=5+(0.28*(nrow(data.file)-10))
+pdf("dotplot.pdf", onefile = FALSE, paper = "special", height = ht, width = wd, pointsize = 2)
+print(pl)
+dev.off()