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csplot.r
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csplot.r
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#!/usr/bin/Rscript
## csplot.r -- Generates a genome-wide plot of data from an input file
## that includes chromosome, location, and value.
## The output is similar to plots used in the WTCCC results paper
## (i.e. dark blue/light blue for different chromosomes), but is split
## over three lines.
## Author: David Eccles (gringer), 2009 <[email protected]>
usage <- function(){
cat("usage: ./csplot.r <file> [options]\n");
cat("\nOther Options:\n");
cat("-help : Only display this help message\n");
cat("-threshold <value> : Only display data greater than <value>\n");
cat("-pointsize <value> : Multiplier for size of points in graph\n");
cat("-invert : Invert values (lowest value at top of graph)\n");
cat("-transparent : Use slightly transparent points\n");
cat("-normlimit : Limit value display to a reasonable normal distribution\n");
cat("-limit <value> : Trim values greater than <limit>\n");
cat("-keep <value> : Keep a proportion of values below the cutoff value\n");
cat("-window <value> : Calculate running median across window of size <value>\n");
cat("-label <string> : Label for Y axis\n");
cat("\n");
}
dataFile <- FALSE; # marker chromosome location <other fields> value
valThreshold <- 0;
useNormDistForMax <- FALSE;
invertAxis <- FALSE;
trimLimit <- FALSE;
transparent <- FALSE;
sizeMul <- 2;
filterKeepProp <- 0; # keep this proportion of markers below threshold cutoff
filterRandom <- (filterKeepProp > 0); # keep a random sampling of markers below threshold cutoff
valueText <- expression(chi^2~Value);
windowSize <- 1;
argLoc <- 1;
while(!is.na(commandArgs(TRUE)[argLoc])){
if(file.exists(commandArgs(TRUE)[argLoc])){ # file existence check
if(dataFile == FALSE){
dataFile <- commandArgs(TRUE)[argLoc];
} else{
cat("Error: More than one input file specified\n",dataFile);
usage();
quit(save = "no", status=1);
}
} else {
parsed <- FALSE;
if(commandArgs(TRUE)[argLoc] == "-help"){
usage();
parsed <- TRUE;
quit(save = "no", status=0);
}
if(commandArgs(TRUE)[argLoc] == "-threshold"){
valThreshold <- as.numeric(commandArgs(TRUE)[argLoc+1]);
argLoc <- argLoc + 1;
cat("Setting value threshold to ",valThreshold,"\n",sep="");
parsed <- TRUE;
}
if(commandArgs(TRUE)[argLoc] == "-pointsize"){
sizeMul <- as.numeric(commandArgs(TRUE)[argLoc+1]);
argLoc <- argLoc + 1;
cat("Setting point size multiplier to ",sizeMul,"\n",sep="");
parsed <- TRUE;
}
if(commandArgs(TRUE)[argLoc] == "-invert"){
invertAxis <- TRUE;
cat("Using normal distribution to set upper graph limit\n");
parsed <- TRUE;
}
if(commandArgs(TRUE)[argLoc] == "-transparent"){
transparent <- TRUE;
cat("Points will have partial transparency\n");
parsed <- TRUE;
}
if(commandArgs(TRUE)[argLoc] == "-normlimit"){
useNormDistForMax <- TRUE;
cat("Using normal distribution to set upper graph limit\n");
parsed <- TRUE;
}
if(commandArgs(TRUE)[argLoc] == "-limit"){
trimLimit <- as.numeric(commandArgs(TRUE)[argLoc+1]);
argLoc <- argLoc + 1;
cat("Values greater than ",trimLimit," will be marked at graph extent\n",sep="");
parsed <- TRUE;
}
if(commandArgs(TRUE)[argLoc] == "-keep"){
filterKeepProp <- as.numeric(commandArgs(TRUE)[argLoc+1]);
argLoc <- argLoc + 1;
filterRandom <- (filterKeepProp > 0);
cat("Including ",filterKeepProp,"x markers below threshold value\n",sep="");
parsed <- TRUE;
}
if(commandArgs(TRUE)[argLoc] == "-window"){
windowSize <- as.numeric(commandArgs(TRUE)[argLoc+1]);
argLoc <- argLoc + 1;
cat("Setting running median window size to ",windowSize,"\n",sep="");
parsed <- TRUE;
}
if(commandArgs(TRUE)[argLoc] == "-label"){
valueText <- commandArgs(TRUE)[argLoc+1];
argLoc <- argLoc + 1;
cat("Setting value text to ",valueText,"\n",sep="");
parsed <- TRUE;
}
if(!parsed){
cat("Error: unknown argument '",commandArgs(TRUE)[argLoc],"'\n",sep="");
}
}
argLoc <- argLoc + 1;
}
if(dataFile == FALSE){
cat("Error: No valid file given\n\n");
usage();
quit(save = "no", status=1);
}
## Chromosome Statistics -- from http://genome.ucsc.edu/goldenPath/stats.html#hg18
cs.stats <-
c(1,247249719,224999719,
2,242951149,237712649,
3,199501827,194704827,
4,191273063,187297063,
5,180857866,177702766,
6,170899992,167273992,
7,158821424,154952424,
8,146274826,142612826,
9,140273252,120143252,
10,135374737,131624737,
11,134452384,131130853,
12,132349534,130303534,
13,114142980,95559980,
14,106368585,88290585,
15,100338915,81341915,
16,88827254,78884754,
17,78774742,77800220,
18,76117153,74656155,
19,63811651,55785651,
20,62435964,59505253,
21,46944323,34171998,
22,49691432,34851332,
23,154913754,151058754, # X
24,57772954,25652954, # Y
25,16571,16571); # MT
dim(cs.stats) <- c(3,25);
cs.stats <- as.data.frame(t(cs.stats));
colnames(cs.stats) <- c("Chromosome","Assembled","Sequenced");
rownames(cs.stats) <- cs.stats$Chromosome;
cs.stats$startPoint <- c(0,cumsum(as.numeric(cs.stats$Assembled)))[-length(cs.stats$Assembled)];
# takes about 10s on melinus with T1D data
cat("Reading data file...", file = stderr());
retVal = grep(pattern = "^\\D+$", x = readLines(dataFile, n = 1), perl = TRUE);
marker.statistics <- NULL;
markers.statistics <- read.table(dataFile, header = (length(retVal) > 0));
colnames(markers.statistics)[1] <- "Marker";
if(length(grep("/",markers.statistics[1,2])) > 0){
colnames(markers.statistics)[2] <- "Mutation";
colnames(markers.statistics)[3] <- "Chromosome";
colnames(markers.statistics)[4] <- "Location";
} else {
colnames(markers.statistics)[2] <- "Chromosome";
colnames(markers.statistics)[3] <- "Location";
}
#rownames(markers.statistics) <- markers.statistics$Marker;
colnames(markers.statistics)[length(colnames(markers.statistics))] <- "Value";
markers.statistics$Chromosome <- sub("chr","",markers.statistics$Chromosome,
ignore.case = TRUE);
markers.statistics$Chromosome <- sub("X","23",markers.statistics$Chromosome,
ignore.case = TRUE);
markers.statistics$Chromosome <- sub("Y","24",markers.statistics$Chromosome,
ignore.case = TRUE);
markers.statistics$Chromosome <- sub("MT?","25",markers.statistics$Chromosome,
ignore.case = TRUE);
markers.statistics$Chromosome <- as.numeric(markers.statistics$Chromosome);
if(transparent){
markers.statistics$Colour <- rep(c("#0000FF80","#00A0FF80"),13)[markers.statistics$Chromosome];
} else {
markers.statistics$Colour <- rep(c("#0000FF","#00A0FF"),13)[markers.statistics$Chromosome];
}
markers.statistics$startPoint <- cs.stats[markers.statistics$Chromosome,]$startPoint;
cat("done!\n", file = stderr());
cat("Calculating limits...", file = stderr());
maxVal <- Inf;
if(useNormDistForMax){ # Filters out abnormally large spikes, redrawn as triangles in graph
maxVal <- 4*qnorm(p = 1 - 1/dim(markers.statistics)[1], mean = mean(markers.statistics$Value), sd = sd(markers.statistics$Value));
}
if(!(trimLimit == FALSE)){
maxVal <- trimLimit;
}
## valRange <- c(min(markers.statistics$Value, na.rm = TRUE),
## min(maxVal, max(markers.statistics$Value, na.rm = TRUE)));
valRange <- c(min(c(0,markers.statistics$Value), na.rm = TRUE),
min(maxVal, max(markers.statistics$Value, na.rm = TRUE)));
markers.statistics$randVal <- runif(dim(markers.statistics)[1]);
markers.filtered <- subset(markers.statistics, (Value >= valThreshold) | (filterRandom & (randVal < filterKeepProp)));
if(transparent){
markers.filtered$Colour[markers.filtered$Value > valRange[2]] <-
rep(c("#80000080","#A0404080"),13)[markers.filtered$Chromosome[markers.filtered$Value > valRange[2]]];
} else {
markers.filtered$Colour[markers.filtered$Value > valRange[2]] <-
rep(c("#800000","#A04040"),13)[markers.filtered$Chromosome[markers.filtered$Value > valRange[2]]];
}
markers.filtered$Value[markers.filtered$Value > valRange[2]] <- valRange[2]+0.01;
cat("done!\n", file = stderr());
cat("Generating png...", file = stderr());
X11.options(antialias="gray");
png("chromosome_plot.png", width = 1280, height = 720, pointsize=12,
antialias="gray");
#svg("chromosome_plot.svg", width = 11, height = 8);
#Cairo_png("chromosome_plot.png", width = 11, height = 8);
if(!(is.expression(valueText)) && (valueText == FALSE)){
par(mfrow = c(3,1), mar = c(4,5,1,1));
} else {
par(mfrow = c(3,1), mar = c(4,7,1,1));
}
assembled.third <- cs.stats$startPoint[23]/3;
drawMarkers <- subset(markers.filtered,
((startPoint + Location) >= assembled.third * 0) &
((startPoint + Location) <= assembled.third * 1));
pchStyle <- (drawMarkers$Value > valRange[2]) + 16; # circles within range, triangles outside
plot(runmed(drawMarkers$startPoint+drawMarkers$Location, windowSize),
drawMarkers$Value, col = drawMarkers$Colour,
pch = pchStyle, cex = 0.5 * sizeMul, xaxt = "n", frame.plot = FALSE,
ylab = "", ylim = valRange, xlim = c(0, assembled.third * 1),
cex.axis = 2, lwd = 2, cex.lab = 2, xaxs = "i",
xlab = "", las = 1);
## print tick marks
axis(side = 1, at=cs.stats$startPoint[c(-24,-25)], labels = FALSE, lwd = 2);
## print labels
axis(side = 1, at=(cs.stats$startPoint[c(-23,-24,-25)] +
cs.stats$startPoint[c(-1,-24,-25)]) / 2, srt = 2,
labels = seq(1,22), las = 1, tick = FALSE, lwd = 2, cex.axis = 2);
drawMarkers <- subset(markers.filtered,
((startPoint + Location) >= assembled.third * 1) &
((startPoint + Location) <= assembled.third * 2));
pchStyle <- (drawMarkers$Value > valRange[2]) + 16; # circles within range, triangles outside
plot(runmed(drawMarkers$startPoint+drawMarkers$Location, windowSize),
drawMarkers$Value, col = drawMarkers$Colour,
pch = pchStyle, cex = 0.5 * sizeMul, xaxt = "n", frame.plot = FALSE,
ylab = valueText, ylim = valRange, xlim = c(assembled.third * 1, assembled.third * 2),
cex.axis = 2, lwd = 5, cex.lab = 2, xaxs = "i",
xlab = "", las = 1, mgp = c(5,1,0));
## print tick marks
axis(side = 1, at=cs.stats$startPoint[c(-24,-25)], labels = FALSE, lwd = 2,
cex.axis = 2);
## print labels
axis(side = 1, at=(cs.stats$startPoint[c(-23,-24,-25)] +
cs.stats$startPoint[c(-1,-24,-25)]) / 2,
labels = seq(1,22), las = 1, tick = FALSE, lwd = 2, cex.axis = 2);
drawMarkers <- subset(markers.filtered,
((startPoint + Location) >= assembled.third * 2) &
((startPoint + Location) <= assembled.third * 3));
pchStyle <- (drawMarkers$Value > valRange[2]) + 16; # circles within range, triangles outside
plot(runmed(drawMarkers$startPoint+drawMarkers$Location, windowSize),
drawMarkers$Value, col = drawMarkers$Colour,
pch = pchStyle, cex = 0.5 * sizeMul, xaxt = "n", frame.plot = FALSE,
ylab = "", ylim = valRange, xlim = c(assembled.third * 2, assembled.third * 3),
cex.axis = 2, cex.lab = 2, xaxs = "i",
xlab = paste("Chromosome location",
if((valThreshold > 0) && (!filterRandom)){paste(", Value >", valThreshold)}, sep = ""), las = 1);
## print tick marks
axis(side = 1, at=cs.stats$startPoint[c(-24,-25)], labels = FALSE, lwd = 2,
cex.axis = 2);
## print labels
axis(side = 1, at=(cs.stats$startPoint[c(-23,-24,-25)] +
cs.stats$startPoint[c(-1,-24,-25)]) / 2,
labels = seq(1,22), las = 1, tick = FALSE, lwd = 2, cex.axis = 2);
dummy <- dev.off();
cat("done!\n", file = stderr());