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repaver.r
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repaver.r
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#!/usr/bin/Rscript
## repaver.r - REpetitive PAttern Visualiser for Extremely-long Reads
outputStyle <- "semicircular"; ## dotplot, circular, semicircular, profile
outputType <- "png";
kmerLength <- 17;
filePrefix <- "repaver";
bgColour <- "#FFFFFF"; # dusk: '#202080'
fileName <- "";
dnaSeqFile <- "data/circ-Nb-ec3-mtDNA.fasta";
## helper R functions
fib.divs <- round(10^((0:4)/5) * 2) * 0.5; ## splits log decades into 5
valToSci <- function(val, unit = ""){
sci.prefixes <- c("", "k", "M", "G", "T", "P", "E", "Z", "Y");
units <- rep(paste(sci.prefixes,unit,sep=""), each=3);
logRegion <- floor(log10(val))+1;
conv.units <- units[logRegion];
conv.div <- 10^rep(0:(length(sci.prefixes)-1) * 3, each = 3)[logRegion];
conv.val <- val / conv.div;
conv.val[val == 0] <- 0;
conv.units[val == 0] <- unit;
return(sprintf("%s %s",conv.val,conv.units));
}
usage <- function(){
cat("usage: ./repaver.r",
"<fasta/fastq file> [options]\n");
cat("\nOther Options:\n");
cat("-help : Only display this help message\n");
cat("-k <int> : Set kmer length\n");
cat("-bg <string> : Background colour\n");
cat("-style <string> : Output file style",
"(dotplot|profile|circular|semicircular)\n");
cat("-type <string> : Output file type (png|svg)\n");
cat("-prefix <string> : Output file prefix (default: 'repaver')\n");
cat("\n");
}
argLoc <- 1;
if(length(commandArgs(TRUE)) < 1){
usage();
quit(save = "no", status=0);
}
while(!is.na(commandArgs(TRUE)[argLoc])){
if(file.exists(commandArgs(TRUE)[argLoc])){ # file existence check
dnaSeqFile <- commandArgs(TRUE)[argLoc];
} else {
if(commandArgs(TRUE)[argLoc] == "-help"){
usage();
quit(save = "no", status=0);
}
else if(commandArgs(TRUE)[argLoc] == "-k"){
kmerLength <- as.numeric(commandArgs(TRUE)[argLoc+1]);
argLoc <- argLoc + 1;
}
else if(commandArgs(TRUE)[argLoc] == "-type"){
outputType <- commandArgs(TRUE)[argLoc+1];
argLoc <- argLoc + 1;
}
else if(commandArgs(TRUE)[argLoc] == "-style"){
outputStyle <- commandArgs(TRUE)[argLoc+1];
argLoc <- argLoc + 1;
}
else if(commandArgs(TRUE)[argLoc] == "-bg"){
bgColour <- commandArgs(TRUE)[argLoc+1];
argLoc <- argLoc + 1;
}
else if(commandArgs(TRUE)[argLoc] == "-prefix"){
filePrefix <- commandArgs(TRUE)[argLoc+1];
argLoc <- argLoc + 1;
}
else {
cat("Error: Argument '",commandArgs(TRUE)[argLoc],
"' is not understood by this program\n\n", sep="");
usage();
quit(save = "no", status=0);
}
}
argLoc <- argLoc + 1;
}
if(!(outputStyle %in% c("dotplot","profile","circular","semicircular"))){
cat("Error: Plot style should be one of ",
"'(dotplot|profile|circular|semicircular)'\n");
usage();
quit(save = "no", status=0);
}
if(!(outputType %in% c("svg","png"))){
cat("Error: File output type should be one of ",
"'(svg|png)'\n");
usage();
quit(save = "no", status=0);
}
library(reticulate);
## Create python function to quickly generate a kmer location
## dictionary and determine the distance from kmers that have been seen before
## This is chunked into no more than ~5000 pieces so that the final image
## generation is slightly quicker.
py_run_string("
from string import maketrans
from Bio import SeqIO
from collections import defaultdict
compTransTable = maketrans('ACGTUYRSWMKDVHBXNacgtuyrswmkdvhbxn',
'TGCAARYSWKMHBDVXNtgcaaryswkmhbdvxn');
def comp(seq):
return(seq.translate(compTransTable))
def rev(seq):
return(seq[::-1])
def rc(seq):
return(seq.translate(compTransTable)[::-1])
def getKmerLocs(seqFile, kSize=17):
fileChunks = dict()
for record in SeqIO.parse(seqFile, \"fastq\" if (('.fq' in seqFile) or ('.fastq' in seqFile)) else \"fasta\"):
kmers = defaultdict(set)
chunks = dict()
chunks['F'] = defaultdict(set)
chunks['R'] = defaultdict(set)
chunks['RC'] = defaultdict(set)
chunks['C'] = defaultdict(set)
seq = str(record.seq)
seqLen = len(seq) ## add in length, because it's cheap
baseBlockSize = int(seqLen / 5000) ## limit to 5000 position slots
if(baseBlockSize < 1):
baseBlockSize = 1
for k, v in zip([seq[d:d+kSize] for d in
xrange(len(seq)-kSize+1)], xrange(len(seq)-kSize+1)):
if((not 'N' in k) and (not 'n' in k)):
krev = k[::-1]
kcomp = comp(k)
krc = kcomp[::-1]
checkstr = {'F': k, 'R': krev, 'C': kcomp, 'RC':krc}
chunkID = 'b' + str(int(v / baseBlockSize) * baseBlockSize)
for type,ko in checkstr.iteritems():
if(ko in kmers):
for p in kmers[ko]:
chunks[type][chunkID].add(v-p)
kmers[k].add(v)
for k, v in chunks.iteritems():
chunks[k] = {kv:list(vv) for kv,vv in chunks[k].iteritems()}
yield(dict({'name': record.id, 'len':seqLen,
'blockSize':baseBlockSize,
'chunks':chunks}))
");
## Generate filtered kmer location dictionary
fileName <- sprintf("%s_k%d_%%03d.%s",filePrefix, kmerLength, outputType);
fileCounter <- 1;
if(outputStyle %in% c("profile", "semicircular")){
if(outputType == "svg"){
svg(filename=fileName, width=20, height=11.25, pointsize=22);
} else {
png(filename=fileName, width=1920, height=1080,
pointsize=22, antialias="gray");
}
} else {
if(outputType == "svg"){
svg(filename=fileName, width=11.25, height=11.25, pointsize=18);
} else {
png(filename=fileName, width=1080, height=1080,
pointsize=18, antialias="gray");
}
}
getLocsIter <- py$getKmerLocs(dnaSeqFile, as.integer(kmerLength));
my.time <- Sys.time();
cat("Generating chunk difference dictionary... ");
while(!is.null(dnaSeqMap <- iter_next(getLocsIter))){
dnaSeqMapName <- dnaSeqMap$name;
cat(sprintf(" done [%s] in %0.2f %s\n",
dnaSeqMapName,
Sys.time() - my.time,
attr(Sys.time() - my.time, "units")));
sLen <- dnaSeqMap$len;
sBS <- dnaSeqMap$b;
cat(sprintf("Processing %s [length: %d; %d bases per block]\n",
dnaSeqMapName, sLen, sBS));
if(outputStyle == "dotplot"){
par(mgp=c(2,0.5,0), bg=bgColour);
plot(NA, xlim=c(0,sLen), ylim=c(sLen,0),
xlab=ifelse(sLen >= 10^6, "Base Location (Mb)",
"Base Location (kb)"),
ylab=ifelse(sLen >= 10^6, "Base Location (Mb)",
"Base Location (kb)"),
axes=FALSE,
main=sprintf("%s (k=%d)", dnaSeqMapName, kmerLength));
if(sLen >= 10^6){
axis(1, at=axTicks(1), labels=pretty(axTicks(1))/10^6);
axis(2, at=rev(axTicks(2)), labels=pretty(axTicks(2))/10^6);
} else {
axis(1, at=axTicks(1), labels=pretty(axTicks(1))/1000);
axis(2, at=rev(axTicks(2)), labels=pretty(axTicks(2))/1000);
}
} else if(outputStyle == "profile"){
par(mgp=c(2.5,1,0), mar=c(4,6,3,0.5),
cex.axis=1.5, cex.lab=1.5, cex.main=2, bg=bgColour);
plot(NA, xlim=c(0,sLen), ylim=c(1,sLen), log="y",
xlab=ifelse(sLen >= 10^6,
"Base Location (Mb)", "Base Location (kb)"),
ylab="",
axes=FALSE,
main=sprintf("%s (k=%d)", dnaSeqMapName, kmerLength));
if(sLen >= 10^6){
axis(1, at=axTicks(1), labels=pretty(axTicks(1))/10^6, lwd=3);
} else {
axis(1, at=axTicks(1), labels=pretty(axTicks(1))/1000, lwd=3);
}
drMax <- ceiling(log10(sLen));
axis(2, at= 10^(0:drMax), las=2, lwd=3, cex.axis=1.5,
labels=valToSci(10^(0:drMax)));
axis(2, at= rep(1:9, each=drMax+1) * 10^(0:drMax), labels=FALSE);
abline(h=10^(0:drMax), col="#80808050", lwd = 3);
mtext("Feature distance (bp)", 2, line=4.5, cex=1.5);
} else if(outputStyle == "circular"){
par(mgp=c(2.5,1,0), mar=c(2.5,2,1.5,2),
cex.axis=1.5, cex.lab=1.5, cex.main=2, bg=bgColour);
plot(NA, xlim=c(-1.1,1.1), ylim=c(-1.2,1),
axes=FALSE, xlab="", ylab="",
main=sprintf("%s (k=%d)", dnaSeqMapName, kmerLength));
} else if(outputStyle == "semicircular"){
par(mgp=c(2.5,1,0), mar=c(2.5,2,2.5,2), bg=bgColour,
cex.axis=1.5, cex.lab=1.5, cex.main=2);
xMul <- (1.2 / par()$pin[2]) * par()$pin[1];
plot(NA, xlim=c(-xMul/2, xMul/2), ylim=c(-0.2, 1),
axes=FALSE, xlab="", ylab="",
main=sprintf("%s (k=%d)", dnaSeqMapName, kmerLength));
}
## f,c,rc,r : red, orange, blue, green
plotPoints <- NULL;
dc <- dnaSeqMap$chunks;
for(type in as.character(names(dnaSeqMap$chunks)[sapply(dc,length)>0])){
if(length(dc[[type]]) == 0){
next;
}
my.time <- Sys.time();
cat(sprintf("Processing %s... ",
c(F="repeats", C="complements",
RC="reverse complements", R="reverses")[type]));
collectFunc <- function(kposs){
vals=dc[[type]][[kposs]];
data.frame(y=rep(as.numeric(substring(kposs,2)),
length(vals)),
dist=vals,
type=rep(type, length(vals)),
stringsAsFactors=FALSE);
}
plotPoints <-
rbind(plotPoints,
Reduce(rbind,
sapply(names(dc[[type]]), simplify=FALSE,
collectFunc)));
cat(sprintf(" done in %0.2f %s\n", Sys.time() - my.time,
attr(Sys.time() - my.time, "units")));
}
plotPoints$x <- plotPoints$y - plotPoints$dist;
my.time <- Sys.time();
cat("Drawing plot... ");
if(outputStyle == "dotplot"){
points(plotPoints, pch=15,
col=c(F="#8b000040",RC="#FF7F0040",
C="#0000FF40",R="#00A00040")[plotPoints$type], cex=0.5);
legend("bottomleft",
legend=c("Forward","Complement","RevComp","Reverse"),
fill=c("#8b000040","#0000FF40","#FF7F0040","#00A00040"),
bg="#FFFFFFE0", inset=0.05);
} else if(outputStyle == "profile"){
## left symbols
points(x=plotPoints$x, y=plotPoints$dist, pch=15,
col=c(F="#9000A040",RC="#FF7F0040",
C="#00A09040",R="#A0900040")[plotPoints$type], cex=0.5);
## right symbols
points(x=plotPoints$y, y=plotPoints$dist, pch=15,
col=c(F="#8b000040",RC="#FDC08640",
C="#0000FF40",R="#00A00040")[plotPoints$type], cex=0.5);
legend(x = "bottom",
fill=c("#9000a0","#8b0000",
"#00a090","#0000ff",
"#ff7f00","#fdc086",
"#a09000","#00a000"),
legend=c("Repeat (L)", "Repeat (R)",
"Comp (L)", "Comp (R)",
"RevComp (L)", "RevComp (R)",
"Reverse (L)", "Reverse (R)"),
bg="#FFFFFFE0", horiz=FALSE, inset=0.01, ncol=4);
} else if(outputStyle == "circular"){
distFlips <- (plotPoints$dist > sLen/2);
plotPoints[distFlips,c("x","y","dist")] <-
plotPoints[distFlips,c("y","x","dist")];
plotPoints$dist[distFlips] <- (sLen - plotPoints$dist[distFlips]);
## Convert distance to radius. This is a piecewise function
## with the following properties:
## * Starts off as a log function
## * Remainder is a linear function
## * The transition point is the point where the slope is equal
## * The transition point is 1/3 along the radius
## * The plot ends at (sLen/2, 1)
## * The base of the log is sLen/12
## Note: slope of log[b](x) = 1/(x*log(b))
pwFun <- function(d){
a <- sLen/50; ## changes to linear approximately 1/3 of the way in
aProp <- (sLen / 2) / a;
ifelse(d < a,
log(d) / log(a),
d/(a * log(a)) + (1 - 1/log(a))) /
((aProp-1) / log(a) + 1) * 0.75 + 0.25;
}
cat("converting distances... ");
plotPoints$r <- pwFun(plotPoints$dist);
cat("drawing points... ");
drMax <- ceiling(log10(sLen));
scalePtsMajor <- rep(1, each=drMax+1) * 10^(0:drMax);
scalePtsMajor <- c(scalePtsMajor[scalePtsMajor < sLen/2], sLen/2);
scalePts <- rep(1:9, each=drMax+1) * 10^(0:drMax);
scalePts <- scalePts[scalePts <= sLen/2];
for(p in scalePtsMajor){ # rings for log scale
points(x=pwFun(p)*cos(seq(0,2*pi, length.out=360)),
y=pwFun(p)*sin(seq(0,2*pi, length.out=360)),
type="l", lwd=3, col="#808080A0");
}
distPts <- (1:99)*10^(drMax-2);
distPts <- c(head(distPts[distPts < sLen], -1), sLen);
if(length(distPts) > 20){
distPts <- (1:9)*10^(drMax-1);
distPts <- signif(c(distPts[distPts < sLen], sLen),3);
}
segments(x0=0.18*cos(distPts / sLen * 2*pi), # tick marks
x1=0.2*cos(distPts / sLen * 2*pi),
y0=0.18*sin(distPts / sLen * 2*pi),
y1=0.2*sin(distPts / sLen * 2*pi),
lwd=2, col="#000000A0");
for(dpi in seq_along(distPts)){ # tick labels for base location
text(x=0.14*cos(distPts[dpi] / sLen * 2*pi),
y=0.14*sin(distPts[dpi] / sLen * 2*pi),
labels=valToSci(signif(distPts[dpi],3)), cex=0.5,
srt=if((distPts[dpi]/sLen * 360 >= 90) &&
(distPts[dpi]/sLen * 360 < 270)){
(distPts[dpi]/sLen * 360 + 180);
} else {
(distPts[dpi]/sLen * 360);
},
col="black");
}
points(x=0.2*cos(seq(10^(drMax-2)/sLen * 2*pi/2,
2*pi, length.out=360)),
y=0.2*sin(seq(10^(drMax-2)/sLen * 2*pi/2,
2*pi, length.out=360)),
type="l", lwd=3, col="#000000A0"); # tick circle
## left symbols
points(plotPoints$r*cos(plotPoints$x/sLen*2*pi),
plotPoints$r*sin(plotPoints$x/sLen*2*pi),
pch=ifelse(outputType=="png",20,"•"),
col=c(F="#9000A040",RC="#FF7F0040",
C="#00A09040",R="#A0900040")[plotPoints$type],
cex=ifelse(outputType=="png",0.5,1));
## right symbols
points(plotPoints$r*cos(plotPoints$y/sLen*2*pi),
plotPoints$r*sin(plotPoints$y/sLen*2*pi),
pch=ifelse(outputType=="png",20,"•"),
col=c(F="#8b000040",RC="#FDC08640",
C="#0000FF40",R="#00A00040")[plotPoints$type],
cex=ifelse(outputType=="png",0.5,1));
rect(xleft=pwFun(head(scalePtsMajor,1))-0.025,
xright=pwFun(tail(scalePtsMajor,1))+0.05,
ytop=0.13, ybottom=-0.13, col="#FFFFFFA0", border=NA);
arrows(x0=pwFun(head(scalePts,-1)), x1=pwFun(tail(scalePts,-1)),
y0=0, angle=90, code=3, length=0.1, lwd=2, col="#80808080");
arrows(x0=pwFun(head(scalePtsMajor,-1)),
x1=pwFun(tail(scalePtsMajor,-1)),
y0=0, angle=90, code=3, length=0.15, lwd=3, col="#00000080");
text(x=pwFun(scalePtsMajor), y=0, col="black",
labels=valToSci(signif(scalePtsMajor,2)), pos=1, offset=1,
cex=0.5);
text(x=mean(range(pwFun(scalePtsMajor))), y=0, col="black",
labels="Feature Distance (bases)", pos=3, offset=1, cex=0.75);
text(x=0, y=0, labels="Sequence\nLocation\n(bases)", col="black",
cex=0.75);
legend(x = "bottom",
fill=c("#9000a0","#8b0000",
"#00a090","#0000ff",
"#ff7f00","#fdc086",
"#a09000","#00a000"),
legend=c("Repeat (L)", "Repeat (R)",
"Comp (L)", "Comp (R)",
"RevComp (L)", "RevComp (R)",
"Reverse (L)", "Reverse (R)"),
bg="#FFFFFFE0", horiz=FALSE, inset=0.01, ncol=4);
} else if(outputStyle == "semicircular"){
## Convert distance to radius. This is a piecewise function
## with the following properties:
## * Starts off as a log function
## * Remainder is a linear function
## * The transition point is the point where the slope is equal
## * The transition point is 1/3 along the radius
## * The plot ends at (sLen/2, 1)
## * The base of the log is sLen/12
## Note: slope of log[b](x) = 1/(x*log(b))
pwFun <- function(d){
a <- sLen/25; ## changes to linear approximately 1/3 of the way in
aProp <- sLen / a;
ifelse(d < a,
log(d) / log(a),
d/(a * log(a)) + (1 - 1/log(a))) /
((aProp-1) / log(a) + 1) * 0.75 + 0.25;
}
cat("converting distances... ");
plotPoints$r <- pwFun(plotPoints$dist);
cat("drawing points... ");
drMax <- ceiling(log10(sLen));
scalePtsMajor <- rep(1, each=drMax+1) * 10^(0:drMax);
scalePtsMajor <- c(scalePtsMajor[scalePtsMajor < sLen], sLen);
scalePts <- rep(1:9, each=drMax+1) * 10^(0:drMax);
scalePts <- scalePts[scalePts <= sLen];
for(p in scalePtsMajor){ # rings for log scale
points(x=pwFun(p)*cos(seq(0,pi, length.out=180)),
y=pwFun(p)*sin(seq(0,pi, length.out=180)),
type="l", lwd=3, col="#808080A0");
}
distPts <- (0:99)*10^(drMax-2);
distPts <- c(head(distPts[distPts < sLen], -1), sLen);
if(length(distPts) > 25){
distPts <- (0:9)*10^(drMax-1);
distPts <- signif(c(distPts[distPts < sLen], sLen),3);
}
segments(x0=-0.18*cos(distPts / sLen * pi), # tick marks for circle
x1=-0.2*cos(distPts / sLen * pi),
y0=0.18*sin(distPts / sLen * pi),
y1=0.2*sin(distPts / sLen * pi),
lwd=2, col="#000000A0");
for(dpi in seq_along(distPts)){ # tick labels for base location
text(x=-0.14*cos(distPts[dpi] / sLen * pi),
y=0.14*sin(distPts[dpi] / sLen * pi),
labels=valToSci(signif(distPts[dpi],3)), cex=0.5,
srt=-if((distPts[dpi]/sLen * 180 >= 90) &&
(distPts[dpi]/sLen * 180 < 270)){
(distPts[dpi]/sLen * 180 + 180);
} else {
(distPts[dpi]/sLen * 180);
},
col="black");
}
points(x=0.2*cos(seq(0, pi, length.out=180)),
y=0.2*sin(seq(0, pi, length.out=180)),
type="l", lwd=3, col="#000000A0"); # tick circle
## left symbols
points(-plotPoints$r*cos(plotPoints$x/sLen*pi),
plotPoints$r*sin(plotPoints$x/sLen*pi),
pch=ifelse(outputType=="png",20,"•"),
col=c(F="#9000A040",RC="#FF7F0040",
C="#00A09040",R="#A0900040")[plotPoints$type],
cex=ifelse(outputType=="png",0.5,1));
## right symbols
points(-plotPoints$r*cos(plotPoints$y/sLen*pi),
plotPoints$r*sin(plotPoints$y/sLen*pi),
pch=ifelse(outputType=="png",20,"•"),
col=c(F="#8b000040",RC="#FDC08640",
C="#0000FF40",R="#00A00040")[plotPoints$type],
cex=ifelse(outputType=="png",0.5,1));
## tick marks (left)
arrows(x0=-pwFun(head(scalePts,-1)),
x1=-pwFun(tail(scalePts,-1)),
y0=0, angle=90, code=3, length=0.1, lwd=2, col="#80808080");
arrows(x0=-pwFun(head(scalePtsMajor,-1)),
x1=-pwFun(tail(scalePtsMajor,-1)),
y0=0, angle=90, code=3, length=0.15, lwd=3, col="#00000080");
## tick marks (right)
arrows(x0=pwFun(head(scalePts,-1)),
x1=pwFun(tail(scalePts,-1)),
y0=0, angle=90, code=3, length=0.1, lwd=2, col="#80808080");
arrows(x0=pwFun(head(scalePtsMajor,-1)),
x1=pwFun(tail(scalePtsMajor,-1)),
y0=0, angle=90, code=3, length=0.15, lwd=3, col="#00000080");
text(x=pwFun(scalePtsMajor), y=0, col="black",
labels=valToSci(signif(scalePtsMajor,2)), pos=1, offset=1,
cex=0.65); # tick labels for distance axis
text(x=-pwFun(scalePtsMajor), y=0, col="black",
labels=valToSci(signif(scalePtsMajor,2)), pos=1, offset=1,
cex=0.65); # tick labels for distance axis
text(x=-mean(range(pwFun(scalePtsMajor))), y=-0.05, col="black",
labels="Feature Distance (bases)", pos=1, offset=1, cex=1);
text(x=mean(range(pwFun(scalePtsMajor))), y=-0.05, col="black",
labels="Feature Distance (bases)", pos=1, offset=1, cex=1);
text(x=0, y=0, labels="Sequence\nLocation\n(bases)", col="black",
cex=1);
legend(x = "bottom",
fill=c("#9000a0","#8b0000",
"#00a090","#0000ff",
"#ff7f00","#fdc086",
"#a09000","#00a000"),
legend=c("Repeat (L)", "Repeat (R)",
"Comp (L)", "Comp (R)",
"RevComp (L)", "RevComp (R)",
"Reverse (L)", "Reverse (R)"),
bg="#FFFFFF80", horiz=FALSE, inset=0.01, ncol=4);
}
cat(sprintf(" done in %0.2f %s\n", Sys.time() - my.time,
attr(Sys.time() - my.time, "units")));
cat("Written to '",sprintf(fileName,fileCounter),"'\n",sep="");
fileCounter <- fileCounter+1;
my.time <- Sys.time();
cat("Generating chunk difference dictionary... ");
}
invisible(dev.off());
cat("finished!\n");