'R: Empty PNG plot
I want to save a plot as PNG. I wrote a for loop to create a graphic image and heatmap before saving it to PNG. My PNG file is blank.
library(SGSeq)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(BSgenome.Hsapiens.UCSC.hg19)
library(org.Hs.eg.db)
# Plot splice variant(s) unique to N60
var.n60.samFile <- subset(samFile, sample_name %in% "N60")
# For each of the 15 genes, subset the Granges objects by only the gene
for (i in gene.list$entrez) {
# Skip gene AQP8 (Entrez ID: 343)
if (i=="343") {
next
}
else{
grange.subset <- txf_grange[txf_grange$geneName %in% i]
# Collapse the ranges of the genes into a single vector
grange.subset <- unlist(IRanges::reduce(split(grange.subset, grange.subset$geneName)))
# Run analyzeFeatures
sgfc_pred <- analyzeFeatures(var.n60.samFile, which=grange.subset)
# Annotate predicted features
sgfc_pred <- SGSeq::annotate(sgfc_pred, txf_ucsc)
# Run analyzeVariants
sgvc_pred <- analyzeVariants(sgfc_pred)
# Plot variants
png("q7plotB.png")
plotVariants(sgvc_pred, eventID=1, color_novel="red")
dev.off()
}
}
Expected output (not exactly the same)
Sources
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