inst/scripts/create-vignette-plots.R

In Bioconductor/SplicingGraphs: Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them

library(SplicingGraphs)

library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
ex_by_tx <- exonsBy(txdb, by="tx", use.names=TRUE)
tx_by_gn <- transcriptsBy(txdb, by="gene")

### Keep only clean genes (i.e. genes with all transcripts on the same
### chromosome and strand).
tx_by_gn <- tx_by_gn[elementNROWS(runValue(seqnames(tx_by_gn))) == 1L]
tx_by_gn <- tx_by_gn[elementNROWS(runValue(strand(tx_by_gn))) == 1L]

### Keep only genes that are on chr19:
is_on_chr19 <- as.character(unlist(runValue(seqnames(tx_by_gn)))) == "chr19"
tx_by_gn <- tx_by_gn[is_on_chr19]

### Compute the splicing graphs (takes about 4 min.):
sg <- SplicingGraphs(ex_by_tx, tx_by_gn)

### Slideshow of the graphs.
slideshow(sg)

#sgraph(sg["100507433"])
#sgraph(sg["10362"])  # gene official symbol: HMG20B
#sgraph(sg["11202"])  # gene official symbol: KLK8 (REVIEWED)
#sgraph(sg["112724"])  # gene official symbol: RDH13 (REVIEWED)
#sgraph(sg["1153"])  # gene official symbol: CIRBP
#sgraph(sg["126259"])  # gene official symbol: TMIGD2
#sgraph(sg["147650"])  # gene official symbol: LINC00085
#sgraph(sg["147965"])  # gene official symbol: FAM98C


### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Plots for CIB3 gene (Entrez ID 117286)
###
### Gene landing page at NCBI: http://www.ncbi.nlm.nih.gov/gene/?term=117286
###

pdf("CIB3-sg.pdf", width=2, height=6)
plot(sgraph(sg["117286"]))
dev.off()

pdf("CIB3-sg2.pdf", width=2.5, height=6)
plot(rsgraph(sg["117286"])
dev.off()

grl <- sg[["117286"]]
### Put the transcripts in an order that is visually more consistent with
### the splicing graph plot.
grl <- grl[c(3L, 2L, 1L, 4L)]
pdf("CIB3-transcripts.pdf", width=6, height=3)
plotTranscripts(grl)
dev.off()


### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Plots for ZNF813 gene (Entrez ID 126017)
###
### Gene landing page at NCBI: http://www.ncbi.nlm.nih.gov/gene/?term=126017

pdf("ZNF813-sg.pdf", width=4, height=6)
plot(sgraph(sg["126017"]))
dev.off()

pdf("ZNF813-sg2.pdf", width=5, height=6)
plot(rsgraph(sg["126017"]))
dev.off()

grl <- sg[["126017"]]
### Put the transcripts in an order that is visually more consistent with
### the splicing graph plot.
grl <- grl[2:1]
pdf("ZNF813-transcripts.pdf", width=6, height=3)
plotTranscripts(grl)
dev.off()


### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Entrez ID 10332 as a complex graph! (10 transcripts, 22 splicing sites)
### graphviz layout engine could do a better job though (in particular edge
### 9-17 doesn't need to cross any other edge).