Hello Jianhong,
Thank you very much for the quick response. I dropped all par commands, and
used layout() instead of par(mfrow=c(4,1)). But, I still get the same error
message. I put the updated code below. Do you have some suggestions on
debugging?
* creating vignettes ... ERROR
--- re-building ‘atsnp-vignette.rmd’ using rmarkdown
Quitting from lines 292-294 (atsnp-vignette.rmd)
Error: processing vignette 'atsnp-vignette.rmd' failed with diagnostics:
invalid graphics state
--- failed re-building ‘atsnp-vignette.rmd’
plot.new()
layout(matrix(c(1,2,3,4), 4, 1, byrow = TRUE))
plotMotifLogo(pcm2pfm(ref_aug_pwm), "Best match to the reference genome",
yaxis=FALSE, xaxis=FALSE, xlab="", ylab="PWM", ...)
if(motif.match$ref_strand=='+') {
arrows((min(which(colSums(ref_aug_pwm)!=0))-1)/ncol(ref_aug_pwm), -0.17,
max(which(colSums(ref_aug_pwm)!=0))/ncol(ref_aug_pwm), -0.17, length = 0.1,
angle = 15, code = 2, col = "blue", lwd = 1.5, xpd=NA)
mtext("5'", 1, adj=(min(which(colSums(ref_aug_pwm)!=0))-1)/ncol(ref_aug_pwm),
padj=1, col="blue", cex=1)
mtext("3'", 1, adj=max(which(colSums(ref_aug_pwm)!=0))/ncol(ref_aug_pwm),
padj=1, col="blue", cex=1)
} else {
arrows(max(which(colSums(ref_aug_pwm)!=0))/ncol(ref_aug_pwm), -0.17,
(min(which(colSums(ref_aug_pwm)!=0))-1)/ncol(ref_aug_pwm), -0.17, length = 0.1,
angle = 15, code = 2, col = "blue", lwd = 1.5, xpd=NA)
mtext("5'", 1, adj=max(which(colSums(ref_aug_pwm)!=0))/ncol(ref_aug_pwm),
padj=1, col="blue", cex=1)
mtext("3'", 1, adj=(min(which(colSums(ref_aug_pwm)!=0))-1)/ncol(ref_aug_pwm),
padj=1, col="blue", cex=1)
}
plotMotifLogo(pcm2pfm(ref_aug_match_pwm), font="mono,Courier", yaxis=FALSE,
xlab="", ylab=paste("(", motif.match$ref_strand, ")", sep=""), ...)
segments(snp_loc/motif.match$snp_ref_length, 0,
snp_loc/motif.match$snp_ref_length, 1, col="blue", lty=3, lwd=2)
segments(snp_loc/motif.match$snp_ref_length, 1,
(snp_loc+1)/motif.match$snp_ref_length, 1, col="blue", lty=3, lwd=2)
segments((snp_loc+1)/motif.match$snp_ref_length, 0,
(snp_loc+1)/motif.match$snp_ref_length, 1, col="blue", lty=3, lwd=2)
segments(snp_loc/motif.match$snp_ref_length, 0,
(snp_loc+1)/motif.match$snp_ref_length, 0, col="blue", lty=3, lwd=2)
if(motif.match$ref_strand=="+") {
mtext("5'", 1, adj=0, padj=1, col="blue", cex=1)
mtext("3'", 1, adj=1, padj=1, col="blue", cex=1)
} else {
mtext("3'", 1, adj=0, padj=1, col="blue", cex=1)
mtext("5'", 1, adj=1, padj=1, col="blue", cex=1)
}
plotMotifLogo(pcm2pfm(snp_aug_match_pwm), "Best match to the SNP genome",
font="mono,Courier", yaxis=FALSE, xlab="", ylab=paste("(",
motif.match$snp_strand, ")", sep=""), ...)
segments(snp_loc/motif.match$snp_ref_length, 0,
snp_loc/motif.match$snp_ref_length, 1, col="blue", lty=3, lwd=2)
segments(snp_loc/motif.match$snp_ref_length, 1,
(snp_loc+1)/motif.match$snp_ref_length, 1, col="blue", lty=3, lwd=2)
segments((snp_loc+1)/motif.match$snp_ref_length, 0,
(snp_loc+1)/motif.match$snp_ref_length, 1, col="blue", lty=3, lwd=2)
segments(snp_loc/motif.match$snp_ref_length, 0,
(snp_loc+1)/motif.match$snp_ref_length, 0, col="blue", lty=3, lwd=2)
if(motif.match$snp_strand=="+") {
mtext("5'", 1, adj=0, padj=1, col="blue", cex=1)
mtext("3'", 1, adj=1, padj=1, col="blue", cex=1)
} else {
mtext("3'", 1, adj=0, padj=1, col="blue", cex=1)
mtext("5'", 1, adj=1, padj=1, col="blue", cex=1)
}
plotMotifLogo(pcm2pfm(snp_aug_pwm), yaxis=FALSE, xaxis=FALSE, xlab="",
ylab="PWM", ...)
if(motif.match$snp_strand=='+') {
arrows((min(which(colSums(snp_aug_pwm)!=0))-1)/ncol(snp_aug_pwm), -0.17,
max(which(colSums(snp_aug_pwm)!=0))/ncol(snp_aug_pwm), -0.17, length = 0.1,
angle = 15, code = 2, col = "blue", lwd = 1.5, xpd=NA)
mtext("5'", 1, adj=(min(which(colSums(snp_aug_pwm)!=0))-1)/ncol(snp_aug_pwm),
padj=1, col="blue", cex=1)
mtext("3'", 1, adj=max(which(colSums(snp_aug_pwm)!=0))/ncol(snp_aug_pwm),
padj=1, col="blue", cex=1)
} else {
arrows(max(which(colSums(snp_aug_pwm)!=0))/ncol(snp_aug_pwm), -0.17,
(min(which(colSums(snp_aug_pwm)!=0))-1)/ncol(snp_aug_pwm), -0.17, length = 0.1,
angle = 15, code = 2, col = "blue", lwd = 1.5, xpd=NA)
mtext("5'", 1, adj=max(which(colSums(snp_aug_pwm)!=0))/ncol(snp_aug_pwm),
padj=1, col="blue", cex=1)
mtext("3'", 1, adj=(min(which(colSums(snp_aug_pwm)!=0))-1)/ncol(snp_aug_pwm),
padj=1, col="blue", cex=1)
}
title(main=paste(motif.match$motif, " Motif Scan for ", motif.match$snpid,
sep=""), outer=TRUE, line=-2, cex.main=cex.main)
}
Best,
Sunyoung
On Apr 23, 2019, at 7:57 AM, Jianhong Ou, Ph.D.
<jianhong...@duke.edu<mailto:jianhong...@duke.edu>> wrote:
Hi Sunyong,
plotMotifLogo does not compatible with par now. Please use grid to plot the
multiple panels in one canvas. I am working on this but it takes time.
Jianhong.
On 4/23/19, 12:47 AM, "Bioc-devel on behalf of Shin, Sunyoung"
<bioc-devel-boun...@r-project.org<mailto:bioc-devel-boun...@r-project.org> on
behalf of sunyoung.s...@utdallas.edu<mailto:sunyoung.s...@utdallas.edu>> wrote:
Dear all,
I got an error message: invalid graphics state as below from BUILD report
for atSNP 0.99.23
(https://urldefense.proofpoint.com/v2/url?u=https-3A__master.bioconductor.org_packages_3.9_bioc_html_atSNP.html&d=DwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=PXg851DHXyo-Gs3eMIfeo49gUXVh-JSZu_MZDDxGun8&m=PbqNdXfVMLxlePSjrHOEN8-tkQLva8Pg6UAfB4VOTUw&s=lESpOegy3zU7jKZUfxiUhG5mSg7qotzhof_KHZmVEB8&e=).
This occurs on every platform: malbec2, tokay2, and celaya2. Running
devtools::check() on my local computer does not produce the error. I would
appreciate it if anyone can help debugging.
* creating vignettes ... ERROR
--- re-building ‘atsnp-vignette.rmd’ using rmarkdown
Quitting from lines 292-294 (atsnp-vignette.rmd)
Error: processing vignette 'atsnp-vignette.rmd' failed with diagnostics:
invalid graphics state
--- failed re-building ‘atsnp-vignette.rmd’
SUMMARY: processing the following file failed:
‘atsnp-vignette.rmd’
Error: Vignette re-building failed.
Execution halted
The graphing function which makes the error is plotMotifMatch(match.seq,
motif.lib = motif_library). Below is the part of the code that is needed to be
fixed, I think.
{
par(mfrow=c(4,1), oma=c(1,1,4,1))
plot.new()
par(mar=c(1.5, 3, 4, 2))
plotMotifLogo(pcm2pfm(ref_aug_pwm), "Best match to the reference genome",
yaxis=FALSE, xaxis=FALSE, xlab="", ylab="PWM", ...)
if(motif.match$ref_strand=='+') {
arrows((min(which(colSums(ref_aug_pwm)!=0))-1)/ncol(ref_aug_pwm), -0.17,
max(which(colSums(ref_aug_pwm)!=0))/ncol(ref_aug_pwm), -0.17, length = 0.1,
angle = 15, code = 2, col = "blue", lwd = 1.5, xpd=NA)
mtext("5'", 1,
adj=(min(which(colSums(ref_aug_pwm)!=0))-1)/ncol(ref_aug_pwm), padj=1,
col="blue", cex=1)
mtext("3'", 1, adj=max(which(colSums(ref_aug_pwm)!=0))/ncol(ref_aug_pwm),
padj=1, col="blue", cex=1)
} else {
arrows(max(which(colSums(ref_aug_pwm)!=0))/ncol(ref_aug_pwm), -0.17,
(min(which(colSums(ref_aug_pwm)!=0))-1)/ncol(ref_aug_pwm), -0.17, length = 0.1,
angle = 15, code = 2, col = "blue", lwd = 1.5, xpd=NA)
mtext("5'", 1, adj=max(which(colSums(ref_aug_pwm)!=0))/ncol(ref_aug_pwm),
padj=1, col="blue", cex=1)
mtext("3'", 1,
adj=(min(which(colSums(ref_aug_pwm)!=0))-1)/ncol(ref_aug_pwm), padj=1,
col="blue", cex=1)
}
par(mar = c(4, 3, 1.5, 2))
plotMotifLogo(pcm2pfm(ref_aug_match_pwm), font="mono,Courier", yaxis=FALSE,
xlab="", ylab=paste("(", motif.match$ref_strand, ")", sep=""), ...)
segments(snp_loc/motif.match$snp_ref_length, 0,
snp_loc/motif.match$snp_ref_length, 1, col="blue", lty=3, lwd=2)
segments(snp_loc/motif.match$snp_ref_length, 1,
(snp_loc+1)/motif.match$snp_ref_length, 1, col="blue", lty=3, lwd=2)
segments((snp_loc+1)/motif.match$snp_ref_length, 0,
(snp_loc+1)/motif.match$snp_ref_length, 1, col="blue", lty=3, lwd=2)
segments(snp_loc/motif.match$snp_ref_length, 0,
(snp_loc+1)/motif.match$snp_ref_length, 0, col="blue", lty=3, lwd=2)
if(motif.match$ref_strand=="+") {
mtext("5'", 1, adj=0, padj=1, col="blue", cex=1)
mtext("3'", 1, adj=1, padj=1, col="blue", cex=1)
} else {
mtext("3'", 1, adj=0, padj=1, col="blue", cex=1)
mtext("5'", 1, adj=1, padj=1, col="blue", cex=1)
}
par(mar=c(1.5, 3, 4, 2))
plotMotifLogo(pcm2pfm(snp_aug_match_pwm), "Best match to the SNP genome",
font="mono,Courier", yaxis=FALSE, xlab="", ylab=paste("(",
motif.match$snp_strand, ")", sep=""), ...)
segments(snp_loc/motif.match$snp_ref_length, 0,
snp_loc/motif.match$snp_ref_length, 1, col="blue", lty=3, lwd=2)
segments(snp_loc/motif.match$snp_ref_length, 1,
(snp_loc+1)/motif.match$snp_ref_length, 1, col="blue", lty=3, lwd=2)
segments((snp_loc+1)/motif.match$snp_ref_length, 0,
(snp_loc+1)/motif.match$snp_ref_length, 1, col="blue", lty=3, lwd=2)
segments(snp_loc/motif.match$snp_ref_length, 0,
(snp_loc+1)/motif.match$snp_ref_length, 0, col="blue", lty=3, lwd=2)
if(motif.match$snp_strand=="+") {
mtext("5'", 1, adj=0, padj=1, col="blue", cex=1)
mtext("3'", 1, adj=1, padj=1, col="blue", cex=1)
} else {
mtext("3'", 1, adj=0, padj=1, col="blue", cex=1)
mtext("5'", 1, adj=1, padj=1, col="blue", cex=1)
}
par(mar=c(4, 3, 1.5, 2))
plotMotifLogo(pcm2pfm(snp_aug_pwm), yaxis=FALSE, xaxis=FALSE, xlab="",
ylab="PWM", ...)
if(motif.match$snp_strand=='+') {
arrows((min(which(colSums(snp_aug_pwm)!=0))-1)/ncol(snp_aug_pwm), -0.17,
max(which(colSums(snp_aug_pwm)!=0))/ncol(snp_aug_pwm), -0.17, length = 0.1,
angle = 15, code = 2, col = "blue", lwd = 1.5, xpd=NA)
mtext("5'", 1,
adj=(min(which(colSums(snp_aug_pwm)!=0))-1)/ncol(snp_aug_pwm), padj=1,
col="blue", cex=1)
mtext("3'", 1, adj=max(which(colSums(snp_aug_pwm)!=0))/ncol(snp_aug_pwm),
padj=1, col="blue", cex=1)
} else {
arrows(max(which(colSums(snp_aug_pwm)!=0))/ncol(snp_aug_pwm), -0.17,
(min(which(colSums(snp_aug_pwm)!=0))-1)/ncol(snp_aug_pwm), -0.17, length = 0.1,
angle = 15, code = 2, col = "blue", lwd = 1.5, xpd=NA)
mtext("5'", 1, adj=max(which(colSums(snp_aug_pwm)!=0))/ncol(snp_aug_pwm),
padj=1, col="blue", cex=1)
mtext("3'", 1,
adj=(min(which(colSums(snp_aug_pwm)!=0))-1)/ncol(snp_aug_pwm), padj=1,
col="blue", cex=1)
}
title(main=paste(motif.match$motif, " Motif Scan for ", motif.match$snpid,
sep=""), outer=TRUE, cex.main=cex.main)
}
Just in case, I added the sessionInfo() of the local run.
sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.3
Matrix products: default
BLAS:
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK:
/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] atSNP_0.99.23 usethis_1.4.0 devtools_2.0.1
Best,
Sunyoung
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