##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:JunctionSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings JunctionSeq_1.18.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/JunctionSeq.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘JunctionSeq/DESCRIPTION’ ... OK
* this is package ‘JunctionSeq’ version ‘1.18.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘JunctionSeq’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
‘Rcpp’ ‘RcppArmadillo’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
prepare_Rd: setJunctionSeqCompiledSourcePackage.Rd:23-25: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'estimateJunctionSeqSizeFactors':
‘...’
Documented arguments not in \usage in documentation object 'fitJunctionSeqDispersionFunction':
‘...’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘JunctionSeq-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: buildAllPlots
> ### Title: Create and save a full battery of JunctionSeq expression plots.
> ### Aliases: buildAllPlots
>
> ### ** Examples
>
>
> data(exampleDataSet,package="JctSeqData");
> buildAllPlots(jscs);
> buildAllPlots: Found 5 genes with at least one significant exon, at adjusted-p-value threshold 0.01
> buildAllPlots: Starting plotting...
> buildAllPlots: Generating Dispersion Plot
Starting device: png (./dispersion-plot.png)
abundance ranges from 0.146009972023612 to 5452.18841073905
dispersion ranges from 1.94121697570967e-06 to 2.08746163174998
Plotting dispersions from 2.71367228072472e-05 to 2.08746163174998
Warning in plot.xy(xy, type, ...) :
semi-transparency is not supported on this device: reported only once per page
> buildAllPlots: Generating MA-Plot (log2FC(CTRL/CASE))
Starting device: png (./ma-plot-log2FC(CTRLvsCASE).png)
Warning in int_abline(a = a, b = b, h = h, v = v, untf = untf, ...) :
semi-transparency is not supported on this device: reported only once per page
> buildAllPlots: Writing HTML results index.
Copying default css stylesheet.
Writing html index. Sat Oct 17 02:27:36 2020
Writing formula data. Sat Oct 17 02:27:36 2020
Writing methods data. Sat Oct 17 02:27:36 2020
Writing sample data. Sat Oct 17 02:27:36 2020
Writing dispersion data. Sat Oct 17 02:27:36 2020
Writing summary plots. Sat Oct 17 02:27:36 2020
Compiling data table. Sat Oct 17 02:27:36 2020
Writing data table. Sat Oct 17 02:27:36 2020
Html index complete. Sat Oct 17 02:27:36 2020
Writing pages. Sat Oct 17 02:27:36 2020
Finished all html files. Sat Oct 17 02:27:36 2020
> buildAllPlots: Finished writing HTML results index.
> buildAllPlots: starting geneID: ENSRNOG00000008079 (1 of 5)
starting buildAllPlotsForGene() for geneID: ENSRNOG00000008079
Starting nested heights...
Starting device: png (.//exprTX/1-expr-TX.png)
> pJSRfG(): ENSRNOG00000008079, plot.type: expr (with TX)
Warning in rect(left, top, r, b, angle = angle, density = density, ...) :
semi-transparency is not supported on this device: reported only once per page
Starting device: png (.//expr/1-expr.png)
> pJSRfG(): ENSRNOG00000008079, plot.type: expr
Warning in rect(left, top, r, b, angle = angle, density = density, ...) :
semi-transparency is not supported on this device: reported only once per page
Starting device: png (.//normCountsTX/1-normCts-TX.png)
> pJSRfG(): ENSRNOG00000008079, plot.type: normCounts (with TX)
Warning in rect(left, top, r, b, angle = angle, density = density, ...) :
semi-transparency is not supported on this device: reported only once per page
Starting device: png (.//normCounts/1-normCts.png)
> pJSRfG(): ENSRNOG00000008079, plot.type: normCounts
Warning in rect(left, top, r, b, angle = angle, density = density, ...) :
semi-transparency is not supported on this device: reported only once per page
Starting device: png (.//rExprTX/1-rExpr-TX.png)
> pJSRfG(): ENSRNOG00000008079, plot.type: rExpr (with TX)
Warning in rect(left, top, r, b, angle = angle, density = density, ...) :
semi-transparency is not supported on this device: reported only once per page
Starting device: png (.//rExpr/1-rExpr.png)
> pJSRfG(): ENSRNOG00000008079, plot.type: rExpr
Warning in rect(left, top, r, b, angle = angle, density = density, ...) :
semi-transparency is not supported on this device: reported only once per page
> buildAllPlots: starting geneID: ENSRNOG00000009281 (2 of 5)
starting buildAllPlotsForGene() for geneID: ENSRNOG00000009281
Starting nested heights...
Starting device: png (.//exprTX/2-expr-TX.png)
> pJSRfG(): ENSRNOG00000009281, plot.type: expr (with TX)
Warning in rect(left, top, r, b, angle = angle, density = density, ...) :
semi-transparency is not supported on this device: reported only once per page
----------- FAILURE REPORT --------------
--- failure: length > 1 in coercion to logical ---
--- srcref ---
:
--- package (from environment) ---
JunctionSeq
--- call from context ---
doTryCatch(return(expr), name, parentenv, handler)
--- call from argument ---
any(c(pw[1] - 1, pw[1] + 1) %in% pwo) && pw%%2 == 0
--- R stacktrace ---
where 1: doTryCatch(return(expr), name, parentenv, handler)
where 2: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 3: tryCatchList(expr, classes, parentenv, handlers)
where 4: tryCatch({
if (debug.mode)
message("> Step 6.9b")
pval.drop <- rep(-pval.height, length(p.values))
pw <- which(p.values != "")
pwo <- pw
while (length(pw) > 0) {
if (any(c(pw[1] - 1, pw[1] + 1) %in% pwo) && pw%%2 ==
0) {
pval.drop[pw[1]] <- pval.drop[pw[1]] + pval.height
}
else {
}
pw <- pw[-1]
}
pval.y <- pval.ceiling + pval.drop
}, error = function(e) {
message("WARNING: staggering p-values failed. Falling back to simpler method. This warning should never appear. If you see this, reporting this to the developer would be appreciated.")
})
where 5: drawPlot(matr = count, ylimn, jscs, intervals, rango, textAxis = y.axis.title,
geneLevelAxisTitle = y.axis.title.right, rt = rt, color.count = color.count,
colorlines = vertline.col, countbinIDs = merged.data$countbinID[rt],
use.vst = use.vst, use.log = use.log, plot.type = plot.type,
main.title = main.title, draw.legend = draw.legend, color.key = color,
condition.names = condition.names, p.values = p.values.labels,
draw.p.values = label.p.vals, plot.lwd = plot.lwd, axes.lwd = axes.lwd,
anno.lwd = anno.lwd, par.cex = par.cex, anno.cex.text = anno.cex.text,
anno.cex.axis = anno.cex.axis, anno.cex.main = anno.cex.main,
fit.countbin.names = fit.countbin.names, debug.mode = debug.mode,
plot.gene.level.expression = plot.gene.level.expression,
geneCount = geneCount, color.geneCount = color.geneCount,
yAxisLabels.inExponentialForm = yAxisLabels.inExponentialForm,
italicize.label = italicize.label, condition.legend.text = condition.legend.text,
annolink.col = annolink.col, exonlty = exonlty, graph.margins = graph.margins,
plotWindowXmax = plotWindowXmax, fit.labels = fit.labels,
...)
where 6: doTryCatch(return(expr), name, parentenv, handler)
where 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 8: tryCatchList(expr, classes, parentenv, handlers)
where 9: tryCatch({
GENE.annotation.height <- GENE.annotation.relative.height *
10
TX.annotation.height <- TX.annotation.relative.height * 10
CONNECTIONS.height <- CONNECTIONS.relative.height * 10
SPLICE.annotation.height <- SPLICE.annotation.relative.height *
10
if (!any(geneID == fData(jscs)$geneID)) {
stop(paste0("FATAL ERROR: GeneID \"", geneID, "\" not found in dataset!"))
}
flat.gff.data <- jscs@flatGffData
merged.data <- fData(jscs)
condition <- jscs@phenoData$condition
exonRescaleFunction <- match.arg(exonRescaleFunction)
sequencing.type <- match.arg(sequencing.type)
splice.junction.drawing.style <- match.arg(splice.junction.drawing.style)
plot.type <- match.arg(plot.type)
truncateBelowOne <- TRUE
if (is.null(plot.exon.results)) {
plot.exon.results <- any(merged.data$featureType == "exonic_part")
}
if (is.null(plot.junction.results)) {
plot.junction.results <- any(merged.data$featureType ==
"splice_site" | merged.data$featureType == "novel_splice_site")
}
if (is.null(plot.novel.junction.results)) {
if (plot.junction.results) {
plot.novel.junction.results <- any(merged.data$featureType ==
"novel_splice_site")
}
else {
plot.novel.junction.results <- FALSE
}
}
flip.splicing <- if (plot.junction.results) {
FALSE
}
else {
TRUE
}
geneName <- jscs@flatGffGeneData$gene_name[jscs@flatGffGeneData$geneID ==
geneID]
if (is.null(condition.legend.text)) {
condition.legend.text <- levels(jscs@phenoData$condition)
names(condition.legend.text) <- condition.legend.text
}
else {
if (is.null(names(condition.legend.text))) {
warning("names(condition.legend.text is NULL! condition.legend.text mis-formatted. Must be a list or character vector, with element names equal to the levels of pData(jscs)$condition. Falling back.")
condition.legend.text <- levels(jscs@phenoData$condition)
names(condition.legend.text) <- condition.legend.text
}
else if (!all(levels(jscs@phenoData$condition) %in% names(condition.legend.text))) {
warning("Not all levels contained in names(condition.legend.text)! condition.legend.text mis-formatted. Must be a list or character vector, with element names equal to the levels of pData(jscs)$condition. Falling back.")
condition.legend.text <- levels(jscs@phenoData$condition)
names(condition.legend.text) <- condition.legend.text
}
}
if (!is.null(jscs@flatGffGeneData[["aggregateGeneStrand"]])) {
geneStrand <- as.character(jscs@flatGffGeneData[["aggregateGeneStrand"]][jscs@flatGffGeneData[["geneID"]] ==
geneID])
txSetString <- as.character(jscs@flatGffGeneData[["tx_set"]][jscs@flatGffGeneData[["geneID"]] ==
geneID])
txStrandString <- as.character(jscs@flatGffGeneData[["tx_strands"]][jscs@flatGffGeneData[["geneID"]] ==
geneID])
txSet <- strsplit(as.character(txSetString), "+", fixed = TRUE)[[1]]
txStrand <- strsplit(as.character(txStrandString), ",",
fixed = TRUE)[[1]]
txStrandMap <- as.list(txStrand)
names(txStrandMap) <- txSet
}
else {
txStrandMap <- list()
geneStrand <- "."
}
final.color.list <- overmerge.list(JUNCTIONSEQ.DEFAULT.COLOR.LIST,
colorList)
SIG.VERTLINE.COLOR = final.color.list[["SIG.VERTLINE.COLOR"]]
NOSIG.VERTLINE.COLOR = final.color.list[["NOSIG.VERTLINE.COLOR"]]
UNTESTABLE.VERTLINE.COLOR = final.color.list[["UNTESTABLE.VERTLINE.COLOR"]]
SIG.FEATURE.COLOR = final.color.list[["SIG.FEATURE.COLOR"]]
NOSIG.FEATURE.COLOR = final.color.list[["NOSIG.FEATURE.COLOR"]]
UNTESTABLE.FEATURE.COLOR = final.color.list[["UNTESTABLE.FEATURE.COLOR"]]
EXCLUDED.FEATURE.COLOR = final.color.list[["EXCLUDED.FEATURE.COLOR"]]
SIG.FEATURE.BORDER.COLOR = final.color.list[["SIG.FEATURE.BORDER.COLOR"]]
NOSIG.FEATURE.BORDER.COLOR = final.color.list[["NOSIG.FEATURE.BORDER.COLOR"]]
UNTESTABLE.FEATURE.BORDER.COLOR = final.color.list[["UNTESTABLE.FEATURE.BORDER.COLOR"]]
EXCLUDED.FEATURE.BORDER.COLOR = final.color.list[["EXCLUDED.FEATURE.BORDER.COLOR"]]
SIG.FEATURE.FILL.COLOR = final.color.list[["SIG.FEATURE.FILL.COLOR"]]
NOSIG.FEATURE.FILL.COLOR = final.color.list[["NOSIG.FEATURE.FILL.COLOR"]]
UNTESTABLE.FEATURE.FILL.COLOR = final.color.list[["UNTESTABLE.FEATURE.FILL.COLOR"]]
EXCLUDED.FEATURE.FILL.COLOR = final.color.list[["EXCLUDED.FEATURE.FILL.COLOR"]]
PLOTTING.LINE.COLORS = final.color.list[["PLOTTING.LINE.COLORS"]]
gene.level.buffer <- 0.5
if (is.null(plot.gene.level.expression)) {
if (use.vst) {
plot.gene.level.expression <- FALSE
}
else {
plot.gene.level.expression <- TRUE
}
}
if (plot.gene.level.expression && use.vst) {
warning("WARNING: plotting of gene-level expression is not supported for vst-transformed plots. Errors are likely to follow.")
}
FDR <- colorRed.FDR.threshold
if (verbose) {
displayTXstring <- if (displayTranscripts)
" (with TX)"
else ""
message("> pJSRfG(): ", geneID, ", plot.type: ", plot.type,
displayTXstring)
}
chrom.label <- as.character(merged.data$chr[merged.data$geneID ==
geneID][1])
rt <- merged.data$geneID == geneID
if (!plot.exon.results) {
if (debug.mode)
message("> Removing ", sum(rt & merged.data$featureType ==
"exonic_part"), " exonic_part features. ", sum(rt &
merged.data$featureType != "exonic_part"), " features remaining")
rt <- rt & merged.data$featureType != "exonic_part"
}
if (!plot.junction.results) {
if (debug.mode)
message("> Removing ", sum(rt & merged.data$featureType ==
"splice_site"), " splice_site features. ", sum(rt &
merged.data$featureType != "splice_site"), " features remaining")
rt <- rt & merged.data$featureType != "splice_site"
}
if (!plot.novel.junction.results) {
if (debug.mode)
message("> Removing ", sum(rt & merged.data$featureType ==
"novel_splice_site"), " novel_splice_site features. ",
sum(rt & merged.data$featureType != "novel_splice_site"),
" features remaining")
rt <- rt & merged.data$featureType != "novel_splice_site"
}
untestable.rt <- which(rt & (!merged.data$testable))
if (!plot.untestable.results) {
if (debug.mode)
message("> Removing ", sum(rt & !merged.data$testable),
" untestable features. ", sum(rt & merged.data$testable),
" features remaining")
rt <- rt & merged.data$testable
}
if (debug.mode)
message("> Plotting ", sum(rt), " features.")
rt <- which(rt)
if (length(rt) == 0) {
message("NO FEATURES TO PLOT!")
}
else {
rt.allExon <- which(flat.gff.data$gene_id == geneID &
flat.gff.data$featureType == "exonic_part")
rango.allExon <- 1:length(rt.allExon)
rt.allJunction <- which(flat.gff.data$gene_id == geneID &
(flat.gff.data$featureType == "splice_site" | flat.gff.data$featureType ==
"novel_splice_site"))
rango.allJunction <- 1:length(rt.allJunction)
rescale.iv <- generate.interval.scale(data.frame(start = c(flat.gff.data$start[rt.allExon],
flat.gff.data$start[rt.allJunction]), end = c(flat.gff.data$end[rt.allExon],
flat.gff.data$end[rt.allJunction]), is.exon = c(rep(TRUE,
length(rt.allExon)), rep(FALSE, length(rt.allJunction)))),
exon.rescale.factor, exonRescaleFunction, debug.mode = debug.mode)
rel <- data.frame(start = rescale.coords(merged.data$start[rt],
rescale.iv), end = rescale.coords(merged.data$end[rt],
rescale.iv))
if (sort.features) {
rt <- rt[order(((rel$end - rel$start)/2) + rel$start)]
}
rango <- 1:length(rt)
draw.legend <- TRUE
condition.names <- levels(condition)
sample.names <- sampleNames(jscs@phenoData)
colorcode.title <- TRUE
numcond <- length(condition.names)
if (debug.mode && verbose)
message("> pJSRforGene(): ", "Reached step 2.")
default.color.list <- PLOTTING.LINE.COLORS
if (numcond > length(default.color.list)) {
message("Too many condition values, the default color selection may not look good! Set your own colors by setting the \"color\" parameter.")
color <- rgb(colorRamp(c("#D7191C", "#FFFFBF", "#2B83BA"))(seq(0,
1, length.out = numcond)), maxColorValue = 255,
alpha = 175)
}
else {
color <- color2transparentVector(default.color.list[1:numcond],
t = 175)
}
if (debug.mode && verbose)
message("> pJSRforGene(): ", "color = ", paste0(color,
collapse = ","))
if (debug.mode && verbose)
message("> pJSRforGene(): ", "length(color) = ",
length(color))
if (debug.mode && verbose)
message("> pJSRforGene(): ", "length(condition.names) = ",
length(condition.names))
if (debug.mode && verbose)
message("> pJSRforGene(): ", "condition.names = ",
paste0(condition.names, collapse = ","))
names(color) <- condition.names
y.axis.title <- ""
main.title <- ""
if (debug.mode && verbose)
message("> pJSRforGene(): ", "Reached step 3.")
if (truncateBelowOne) {
convertY <- function(y) {
ifelse(y < 0, ifelse(is.infinite(y), INTERNAL.NINF.VALUE,
(1 - exp(y)) * INTERNAL.NINF.VALUE), y)
}
}
else {
convertY <- function(y) {
y
}
}
if (plot.type == "rExpr") {
count <- if (use.vst) {
vst(jscs@plottingEstimates[["relExprEstimate"]][rt,
, drop = FALSE], jscs)
}
else if (use.log) {
apply(log10(jscs@plottingEstimates[["relExprEstimate"]][rt,
, drop = FALSE]), c(1, 2), FUN = convertY)
}
else {
jscs@plottingEstimates[["relExprEstimate"]][rt,
, drop = FALSE]
}
color.count <- rep(color[condition.names], each = nrow(count))
y.axis.title <- "Relative Coverage"
y.axis.title.right <- "Gene-Level Mean Normalized Counts"
main.title <- paste0("Relative Coverage (", geneName,
")")
if (plot.gene.level.expression) {
geneCount <- if (use.vst) {
plot.gene.level.expression <- FALSE
NULL
}
else if (use.log) {
sapply(log10(jscs@geneLevelPlottingEstimates[["geneLevelEstModeled"]][rownames(jscs@geneLevelPlottingEstimates[["geneLevelEstModeled"]]) ==
geneID, ]), FUN = convertY)
}
else {
jscs@geneLevelPlottingEstimates[["geneLevelEstModeled"]][rownames(jscs@geneLevelPlottingEstimates[["geneLevelEstModeled"]]) ==
geneID, ]
}
color.geneCount <- color[condition.names]
}
}
else if (plot.type == "normCounts") {
count <- if (use.vst) {
vst(jscs@plottingEstimates[["normCounts"]][rt,
1:length(sample.names), drop = FALSE], jscs)
}
else if (use.log) {
apply(log10(jscs@plottingEstimates[["normCounts"]][rt,
1:length(sample.names), drop = FALSE]), c(1,
2), FUN = convertY)
}
else {
jscs@plottingEstimates[["normCounts"]][rt, 1:length(sample.names),
drop = FALSE]
}
if (plot.gene.level.expression) {
geneCount <- if (use.vst) {
plot.gene.level.expression <- FALSE
NULL
}
else if (use.log) {
sapply(log10(jscs@geneCountData[rownames(jscs@geneCountData) ==
geneID, ]/sizeFactors(jscs)), FUN = convertY)
}
else {
jscs@geneCountData[rownames(jscs@geneCountData) ==
geneID, ]/sizeFactors(jscs)
}
color.geneCount <- color[as.character(condition)]
}
color.count <- rep(color[as.character(condition)],
each = nrow(count))
y.axis.title <- "Normalized Counts"
y.axis.title.right <- "Gene-Level Normalized Counts"
main.title <- paste0("Normalized Counts (", geneName,
")")
}
else if (plot.type == "rawCounts") {
count <- if (use.vst) {
vst(jscs@countVectors[rt, 1:length(sample.names),
drop = FALSE], jscs)
}
else if (use.log) {
apply(log10(jscs@countVectors[rt, 1:length(sample.names),
drop = FALSE]), c(1, 2), FUN = function(y) {
max(INTERNAL.NINF.VALUE, y)
})
}
else {
jscs@countVectors[rt, 1:length(sample.names),
drop = FALSE]
}
if (plot.gene.level.expression) {
geneCount <- if (use.vst) {
plot.gene.level.expression <- FALSE
NULL
}
else if (use.log) {
sapply(log10(jscs@geneCountData[rownames(jscs@geneCountData) ==
geneID, ]), FUN = convertY)
}
else {
jscs@geneCountData[rownames(jscs@geneCountData) ==
geneID, ]
}
color.geneCount <- color[as.character(condition)]
}
color.count <- rep(color[as.character(condition)],
each = nrow(count))
y.axis.title <- "Raw Counts"
y.axis.title.right <- "Raw Gene-Level Counts"
main.title <- paste0("Raw Counts (", geneName, ")")
}
else if (plot.type == "expr") {
count <- if (use.vst) {
vst(jscs@plottingEstimates[["exprEstimate"]][rt,
, drop = FALSE], jscs)
}
else if (use.log) {
apply(log10(jscs@plottingEstimates[["exprEstimate"]][rt,
, drop = FALSE]), c(1, 2), FUN = convertY)
}
else {
jscs@plottingEstimates[["exprEstimate"]][rt,
, drop = FALSE]
}
if (plot.gene.level.expression) {
geneCount <- if (use.vst) {
plot.gene.level.expression <- FALSE
NULL
}
else if (use.log) {
sapply(log10(jscs@geneLevelPlottingEstimates[["geneLevelEstModeled"]][rownames(jscs@geneLevelPlottingEstimates[["geneLevelEstModeled"]]) ==
geneID, ]), FUN = convertY)
}
else {
jscs@geneLevelPlottingEstimates[["geneLevelEstModeled"]][rownames(jscs@geneLevelPlottingEstimates[["geneLevelEstModeled"]]) ==
geneID, ]
}
color.geneCount <- color[condition.names]
}
color.count <- rep(color[condition.names], each = nrow(count))
y.axis.title <- "Mean Normalized Counts"
y.axis.title.right <- "Gene-Level Mean Normalized Counts"
main.title <- paste0("Mean Normalized Coverage (",
geneName, ")")
}
else {
stop(paste0("FATAL ERROR: Unknown plot type! plot.type = \"",
plot.type, "\""))
}
fragment.label <- if (sequencing.type == "paired-end")
"Read-Pair"
else "Read"
if (plot.type == "rExpr") {
main.title <- paste0("Relative Coverage (", geneName,
")")
y.axis.title <- paste0("Relative Coverage")
y.axis.title.right <- paste0(fragment.label, "s per Sample, Gene-Level")
}
else if (plot.type == "normCounts") {
main.title <- paste0("Normalized Counts (", geneName,
")")
y.axis.title <- paste0("Normalized Counts")
y.axis.title.right <- paste0("Normalized Counts, Gene-Level")
}
else if (plot.type == "rawCounts") {
main.title <- paste0("Raw Counts (", geneName, ")")
y.axis.title <- paste0("Raw ", fragment.label, " Counts")
y.axis.title.right <- paste0("Raw ", fragment.label,
" Counts, Gene-Level")
}
else if (plot.type == "expr") {
main.title <- paste0("Mean Normalized Coverage (",
geneName, ")")
y.axis.title <- paste0(fragment.label, "s per Sample")
y.axis.title.right <- paste0(fragment.label, "s per Sample, Gene-Level")
}
else {
stop(paste0("FATAL ERROR: Unknown plot type! plot.type = \"",
plot.type, "\""))
}
if (!is.null(title.main))
main.title <- title.main
if (!is.null(title.ylab))
y.axis.title <- title.ylab
if (!is.null(title.ylab.right))
y.axis.title.right <- title.ylab.right
if (!plot.gene.level.expression) {
geneCount <- NULL
color.geneCount <- NULL
}
count <- as.matrix(count)
if (debug.mode && verbose)
message("> pJSRforGene(): ", "Reached step 4.")
intervals <- (0:nrow(count))/nrow(count)
numexons <- nrow(count)
each <- merged.data$padjust[rt]
vertline.col <- ifelse(merged.data$testable[rt], ifelse(f.na(merged.data$padjust[rt] <=
FDR), SIG.VERTLINE.COLOR, NOSIG.VERTLINE.COLOR),
UNTESTABLE.VERTLINE.COLOR)
annolink.col <- ifelse(merged.data$testable[rt], ifelse(f.na(merged.data$padjust[rt] <=
FDR), SIG.FEATURE.COLOR, NOSIG.FEATURE.COLOR), UNTESTABLE.FEATURE.COLOR)
exonlty <- rep(final.color.list[["EXON.CONNECTION.LTY"]],
length(vertline.col))
exonlty[as.character(merged.data$featureType[rt]) ==
"novel_splice_site"] <- final.color.list[["NOVEL.SPLICE.CONNECTION.LTY"]]
exonlty[as.character(merged.data$featureType[rt]) ==
"splice_site"] <- final.color.list[["KNOWN.SPLICE.CONNECTION.LTY"]]
is.sig.feature <- f.na(each <= FDR)
sig.feature <- which(is.sig.feature)
if (debug.mode && verbose)
message("> pJSRforGene(): ", "Reached step 5.")
sub <- data.frame(start = merged.data$start[rt], end = merged.data$end[rt],
chr = merged.data$chr[rt], strand = merged.data$strand[rt],
is.exon = (merged.data$featureType[rt] == "exonic_part"),
is.testable = merged.data$testable[rt], is.sig = is.sig.feature,
col = vertline.col, featureType = merged.data$featureType[rt],
featureID = rownames(merged.data)[rt], stringsAsFactors = FALSE)
sub.allExon <- data.frame(start = flat.gff.data$start[rt.allExon],
end = flat.gff.data$end[rt.allExon], chr = flat.gff.data$chrom[rt.allExon],
strand = flat.gff.data$strand[rt.allExon], is.exon = (flat.gff.data$featureType[rt.allExon] ==
"exonic_part"), featureID = as.character(flat.gff.data$featureName[rt.allExon]),
stringsAsFactors = FALSE)
sub.allJunction <- data.frame(start = flat.gff.data$start[rt.allJunction],
end = flat.gff.data$end[rt.allJunction], chr = flat.gff.data$chrom[rt.allJunction],
strand = flat.gff.data$strand[rt.allJunction], is.exon = (flat.gff.data$featureType[rt.allJunction] ==
"exonic_part"), feature.type = flat.gff.data$featureType[rt.allJunction],
is.novel = (flat.gff.data$featureType[rt.allJunction] ==
"novel_splice_site"), featureID = as.character(flat.gff.data$featureName[rt.allJunction]),
stringsAsFactors = FALSE)
sub.allJunction$is.plotted <- sub.allJunction$featureID %in%
sub$featureID
testable.featureIDs <- sub$featureID[sub$is.testable]
sig.featureIDs <- sub$featureID[sub$is.sig]
untestable.featureIDs <- rownames(merged.data)[untestable.rt]
if (debug.mode && verbose) {
message("testable.featureIDs: ", paste0(testable.featureIDs,
collapse = ","))
}
if (debug.mode && verbose) {
message("sig.featureIDs: ", paste0(sig.featureIDs,
collapse = ","))
}
if (debug.mode && verbose) {
message("untestable.featureIDs: ", paste0(untestable.featureIDs,
collapse = ","))
}
sub.allExon$is.testable <- sub.allExon$featureID %in%
testable.featureIDs
sub.allExon$is.sig <- sub.allExon$featureID %in% sig.featureIDs
sub.allExon$is.untestable <- sub.allExon$featureID %in%
untestable.featureIDs
sub.allJunction$is.testable <- sub.allJunction$featureID %in%
testable.featureIDs
sub.allJunction$is.sig <- sub.allJunction$featureID %in%
sig.featureIDs
sub.allJunction$is.untestable <- sub.allJunction$featureID %in%
untestable.featureIDs
sub.allExon$lineColor <- ifelse(sub.allExon$is.testable,
ifelse(sub.allExon$is.sig, SIG.FEATURE.COLOR, NOSIG.FEATURE.COLOR),
ifelse(sub.allExon$is.untestable, UNTESTABLE.FEATURE.COLOR,
EXCLUDED.FEATURE.COLOR))
sub.allExon$fillColor <- ifelse(sub.allExon$is.testable,
ifelse(sub.allExon$is.sig, SIG.FEATURE.FILL.COLOR,
NOSIG.FEATURE.FILL.COLOR), ifelse(sub.allExon$is.untestable,
UNTESTABLE.FEATURE.FILL.COLOR, EXCLUDED.FEATURE.FILL.COLOR))
sub.allExon$borderColor <- ifelse(sub.allExon$is.testable,
ifelse(sub.allExon$is.sig, SIG.FEATURE.BORDER.COLOR,
NOSIG.FEATURE.COLOR), ifelse(sub.allExon$is.untestable,
UNTESTABLE.FEATURE.BORDER.COLOR, EXCLUDED.FEATURE.BORDER.COLOR))
sub.allJunction$lineColor <- ifelse(sub.allJunction$is.testable,
ifelse(sub.allJunction$is.sig, SIG.FEATURE.COLOR,
NOSIG.FEATURE.COLOR), ifelse(sub.allJunction$is.untestable,
UNTESTABLE.FEATURE.COLOR, EXCLUDED.FEATURE.COLOR))
sub.allJunction$lty <- ifelse(sub.allJunction$is.novel,
final.color.list[["NOVEL.SPLICE.LTY"]], final.color.list[["KNOWN.SPLICE.LTY"]])
sig.feature.names <- sub$featureID[is.sig.feature & sub$is.exon]
allExon.isSig <- sub.allExon$featureID %in% sig.featureIDs
allExon.exonCol <- ifelse(allExon.isSig, "#F219ED", "#CCCCCC")
if (debug.mode == 2 && verbose) {
message("> Debugging Info:")
message(" Exons:")
message(" ", paste0(names(sub.allExon),
collapse = "\t"))
for (i in 1:length(sub.allExon$start)) {
message(" ", paste0(sub.allExon[i,
], collapse = "\t"))
}
message("> dim(count) = ", paste0(dim(count),
collapse = ","))
message("> rt: ", paste0(rt, collapse = ","))
message("> rango: ", paste0(rango, collapse = ","))
message("> ncol(count): ", ncol(count))
}
sub.sig <- sub[sig.feature, , drop = FALSE]
rel.calc.min <- min(sub.allJunction$start, sub.allExon$start)
rel.calc.max <- max(sub.allJunction$end, sub.allExon$end)
transcripts <- sapply(sapply(flat.gff.data$transcripts[rt.allExon],
toString), function(x) {
strsplit(x, "+", fixed = TRUE)
})
trans <- Reduce(union, transcripts)
if (displayTranscripts == TRUE) {
mat <- 1:4
hei <- c(10, CONNECTIONS.height, GENE.annotation.height +
SPLICE.annotation.height, TX.annotation.height *
(length(trans) + TX.margins[1] + TX.margins[2]))
}
else {
mat <- 1:4
hei <- c(10, CONNECTIONS.height, GENE.annotation.height +
SPLICE.annotation.height, TX.annotation.height *
TX.margins[2])
}
layout(matrix(mat), heights = hei)
if (debug.mode && verbose) {
message("> length(trans) = ", length(trans))
message("> FINAL LAYOUT:")
message("> heights = [", paste0(hei, collapse = ","),
"]")
}
if (debug.mode && verbose)
message("> pJSRforGene(): ", "Reached step 6.")
ylimn <- c(min(min(count, na.rm = TRUE), 0), max(count,
na.rm = TRUE))
if ((!use.vst) && use.log)
ylimn[1] <- INTERNAL.NINF.VALUE
p.values.labels <- ifelse(f.na(each <= FDR), format(each,
digits = 3), "")
if (any(sub$is.exon)) {
italicize.label <- !sub$is.exon
}
else {
italicize.label <- NULL
}
plotWindowXmax <- if (plot.gene.level.expression) {
(length(intervals) + 1)/length(intervals)
}
else {
1
}
intervals <- drawPlot(matr = count, ylimn, jscs, intervals,
rango, textAxis = y.axis.title, geneLevelAxisTitle = y.axis.title.right,
rt = rt, color.count = color.count, colorlines = vertline.col,
countbinIDs = merged.data$countbinID[rt], use.vst = use.vst,
use.log = use.log, plot.type = plot.type, main.title = main.title,
draw.legend = draw.legend, color.key = color, condition.names = condition.names,
p.values = p.values.labels, draw.p.values = label.p.vals,
plot.lwd = plot.lwd, axes.lwd = axes.lwd, anno.lwd = anno.lwd,
par.cex = par.cex, anno.cex.text = anno.cex.text,
anno.cex.axis = anno.cex.axis, anno.cex.main = anno.cex.main,
fit.countbin.names = fit.countbin.names, debug.mode = debug.mode,
plot.gene.level.expression = plot.gene.level.expression,
geneCount = geneCount, color.geneCount = color.geneCount,
yAxisLabels.inExponentialForm = yAxisLabels.inExponentialForm,
italicize.label = italicize.label, condition.legend.text = condition.legend.text,
annolink.col = annolink.col, exonlty = exonlty, graph.margins = graph.margins,
plotWindowXmax = plotWindowXmax, fit.labels = fit.labels,
...)
if (debug.mode && verbose)
message("> pJSRforGene(): ", "Reached end of step 6.")
if (debug.mode && verbose)
message("> pJSRforGene(): ", "Reached step 7.")
if (USE.MARGIN.MEX) {
par(mar = c(0, graph.margins[2], 0, graph.margins[4]),
cex = par.cex, mex = anno.cex.text)
}
else {
par(mar = c(0, graph.margins[2], 0, graph.margins[4]),
cex = par.cex)
}
plot.new()
plot.window(xlim = c(0, plotWindowXmax), ylim = c(0,
1), xaxs = "i")
rel <- data.frame(start = rescale.coords(sub$start, rescale.iv),
end = rescale.coords(sub$end, rescale.iv))
connection.lines.bottom <- apply((rbind(rel[rango, 2],
rel[rango, 1])), 2, median) * plotWindowXmax
connection.lines.top <- apply(rbind(intervals[rango],
intervals[rango + 1] - ((intervals[rango + 1] - intervals[rango]) *
0.2)), 2, median)
segments(connection.lines.bottom, 0, connection.lines.top,
1, col = annolink.col, lty = exonlty, lwd = gene.lwd,
cex = anno.cex.text, cex.axis = anno.cex.main, cex.main = anno.cex.main,
xpd = NA, ...)
par(mar = c(1.5, graph.margins[2], 0, graph.margins[4]),
cex = par.cex)
startSites <- c()
endSites <- c()
for (i in 1:length(trans)) {
logicexons <- sapply(transcripts, function(x) {
any(x == trans[i])
})
startSites <- c(startSites, sub.allExon$start[logicexons][1])
endSites <- c(endSites, sub.allExon$end[logicexons][sum(logicexons)])
}
startSites <- unique(startSites)
endSites <- unique(endSites)
drawGene(rel.calc.min, rel.calc.max, tr = sub, tr.allExon = sub.allExon,
tr.allJunction = sub.allJunction, rango, rescale.iv = rescale.iv,
exoncol = annolink.col, allExon.exonCol = allExon.exonCol,
names, trName = "Gene model", anno.cex.text = anno.cex.text,
par.cex = par.cex, exonlty = exonlty, plot.lwd = gene.lwd,
anno.lwd = anno.lwd, show.strand.arrows = show.strand.arrows,
geneStrand = geneStrand, cex.axis = anno.cex.axis,
cex.main = anno.cex.main, draw.untestable.annotation = draw.untestable.annotation,
draw.start.end.sites = draw.start.end.sites, startSites = startSites,
endSites = endSites, cex.arrows = cex.arrows, chrom.label = chrom.label,
label.chromosome = label.chromosome, splice.junction.drawing.style = splice.junction.drawing.style,
draw.nested.SJ = draw.nested.SJ, merge.exon.parts = merge.exon.parts,
plot.untestable.results = plot.untestable.results,
exon.height = GENE.annotation.height/(SPLICE.annotation.height +
GENE.annotation.height), INTERNAL.VARS = INTERNAL.VARS,
flip.splicing = flip.splicing, ...)
include.endpoints.on.coordinates <- FALSE
num.coord.miniticks.per.tick <- 10
if (drawCoordinates) {
if (!is.null(rescale.iv)) {
pretty.x <- pretty(c(rel.calc.min, rel.calc.max),
n = 5)
pretty.interval <- pretty.x[2] - pretty.x[1]
pretty.x <- pretty.x[pretty.x > rel.calc.min &
pretty.x < rel.calc.max]
rescaled.pretty.x <- rescale.coords(pretty.x,
rescale.iv)
if (num.coord.miniticks.per.tick > 0) {
rel.coord.miniticks <- pretty.interval * (1:(num.coord.miniticks.per.tick -
1))/num.coord.miniticks.per.tick
unscaled.coord.miniticks <- unlist(lapply(pretty.x,
function(a) {
a + rel.coord.miniticks
}))
unscaled.coord.miniticks <- c(pretty.x[1] -
rel.coord.miniticks, unscaled.coord.miniticks)
rescaled.coord.miniticks <- rescale.coords(unscaled.coord.miniticks,
rescale.iv) * (rel.calc.max - rel.calc.min) +
rel.calc.min
}
else {
rescaled.coord.miniticks <- FALSE
}
if (include.endpoints.on.coordinates) {
if (min(rescaled.pretty.x) > 0.05) {
pretty.x <- c(rel.calc.min, pretty.x)
rescaled.pretty.x <- c(0, rescaled.pretty.x)
}
if (max(rescaled.pretty.x) < 0.95) {
pretty.x <- c(pretty.x, rel.calc.max)
rescaled.pretty.x <- c(rescaled.pretty.x,
1)
}
}
rescaled.pretty.x <- rescaled.pretty.x * (rel.calc.max -
rel.calc.min) + rel.calc.min
}
else {
pretty.x <- pretty(c(rel.calc.min, rel.calc.max),
n = 5)
coord.miniticks <- FALSE
}
usr <- par("usr")
cxy <- par("cxy")
pretty.x <- sprintf("%0.f", pretty.x)
smallest.width.coordAxis <- min(abs(rescaled.pretty.x[-1] -
rescaled.pretty.x[-length(rescaled.pretty.x)]))
if (fit.genomic.axis) {
anno.cex.coordAxis <- shrink.character.vector(paste0(pretty.x,
"0"), curr.cex = anno.cex.axis, max.width = smallest.width.coordAxis)
if (anno.cex.coordAxis * 2 < anno.cex.axis) {
anno.cex.coordAxis <- anno.cex.axis/2
coordAxis.widths <- abs(rescaled.pretty.x[-1] -
rescaled.pretty.x[-length(rescaled.pretty.x)])
for (i in 2:length(pretty.x)) {
if ((strwidth(pretty.x[i - 1], cex = anno.cex.coordAxis)/2) +
(strwidth(pretty.x[i], cex = anno.cex.coordAxis)/2) >
abs(rescaled.pretty.x[i - 1] - rescaled.pretty.x[i])) {
pretty.x[i] <- ""
}
}
}
}
else {
anno.cex.coordAxis <- anno.cex.axis
}
devlim <- device.limits()
coord.ticks.top <- usr[3]
coord.mainTicks.bottom <- usr[3] - (cxy[2]/2)
coord.text.top <- usr[3] - (cxy[2] * (3/4))
coord.miniTicks.bottom <- coord.ticks.top - abs(coord.mainTicks.bottom -
coord.ticks.top)/2
segments(x0 = rescaled.pretty.x, y0 = usr[3], x1 = rescaled.pretty.x,
y1 = usr[3] - (cxy[2]/2), xpd = NA, lwd = anno.lwd,
...)
lines(c(rel.calc.min, rel.calc.max), c(par("usr")[3],
par("usr")[3]), lwd = axes.lwd, xpd = NA, ...)
segments(x0 = rescaled.coord.miniticks, y0 = usr[3],
x1 = rescaled.coord.miniticks, y1 = usr[3] -
(cxy[2]/4), xpd = NA, lwd = anno.lwd, ...)
text(rescaled.pretty.x, usr[3] - (cxy[2] * (3/4)),
pretty.x, cex = anno.cex.coordAxis, xpd = NA,
adj = c(0.5, 1), ...)
}
if (label.chromosome) {
chrom.label.width.max <- abs(par("usr")[1] - device.limits()[1]) *
0.9
chrom.label.cex <- shrink.character.vector(chrom.label,
curr.cex = anno.cex.text, max.width = chrom.label.width.max)
text(par("usr")[1], par("usr")[3], chrom.label, cex = chrom.label.cex,
adj = c(1.1, 0.5), xpd = NA, font = 2, ...)
}
if (displayTranscripts) {
if (USE.MARGIN.MEX) {
par(cex = par.cex, mar = c(0, graph.margins[2],
0, graph.margins[4]), mex = anno.cex.text)
}
else {
par(cex = par.cex, mar = c(0, graph.margins[2],
0, graph.margins[4]))
}
plot.new()
plot.window(xlim = c(rel.calc.min, rel.calc.max),
ylim = c(-TX.margins[2], length(trans) + TX.margins[1]),
xaxs = "i", yaxs = "i")
for (i in 1:length(trans)) {
ymin <- length(trans) - i
if (include.TX.names) {
trName = trans[i]
}
else {
trName = NULL
}
logicexons <- sapply(transcripts, function(x) {
any(x == trans[i])
})
tr <- sub.allExon[logicexons, ]
curr.exoncol <- ifelse(allExon.isSig[logicexons],
"#F219ED", "#CCCCCC")
drawTranscript(rel.calc.min, rel.calc.max, ymin = ymin,
tr = tr, tr.allJunction = sub.allJunction,
rango = 1:nrow(tr), rescale.iv = rescale.iv,
names = c(), trName = trName, trStrand = txStrandMap[[trName]],
draw.strand = geneStrand == ".", par.cex = par.cex,
anno.cex.text = anno.cex.text, sub.sig = sub.sig,
anno.lwd = gene.lwd, cex.axis = anno.cex.axis,
cex.main = anno.cex.main, cex.arrows = cex.arrows,
...)
}
}
else {
par(mar = c(0, 0, 0, 0))
plot.new()
}
par(mar = c(0, 0, 0, 0))
if (debug.mode && verbose)
message("> pJSRfG(): ", " Done.")
}
}, error = function(e) {
message("Error caught while attempting plotJunctionSeqResultsForGene")
message("---------------------")
message(" Error text:")
message(" ", e)
message("")
message("---------------------")
message(" Input parameters:")
message(" geneID = ", geneID)
message(" plot.type = ", plot.type)
message(" displayTranscripts = ", displayTranscripts)
message("---------------------")
warning("Error caught while attempting plotJunctionSeqResultsForGene")
warning("Error text:")
warning(e)
})
where 10: plotJunctionSeqResultsForGene(geneID, jscs, colorRed.FDR.threshold = FDR,
colorList = colorList, plot.type = plot.type, use.vst = use.vst,
use.log = use.log, exon.rescale.factor = exon.rescale.factor,
displayTranscripts = TRUE, plot.lwd = plot.lwd, axes.lwd = axes.lwd,
anno.lwd = anno.lwd, par.cex = par.cex, anno.cex.text = anno.cex.text,
plot.exon.results = plot.exon.results, plot.junction.results = plot.junction.results,
plot.novel.junction.results = plot.novel.junction.results,
plot.untestable.results = plot.untestable.results, anno.cex.axis = anno.cex.axis,
anno.cex.main = anno.cex.main, drawCoordinates = drawCoordinates,
graph.margins = graph.margins, yAxisLabels.inExponentialForm = yAxisLabels.inExponentialForm,
plot.gene.level.expression = plot.gene.level.expression,
condition.legend.text = condition.legend.text, include.TX.names = include.TX.names,
GENE.annotation.relative.height = GENE.annotation.relative.height,
TX.annotation.relative.height = TX.annotation.relative.height,
draw.start.end.sites = draw.start.end.sites, show.strand.arrows = show.strand.arrows,
debug.mode = debug.mode, sequencing.type = sequencing.type,
gene.lwd = gene.lwd, CONNECTIONS.relative.height = CONNECTIONS.relative.height,
TX.margins = TX.margins, SPLICE.annotation.relative.height = SPLICE.annotation.relative.height,
draw.nested.SJ = draw.nested.SJ, INTERNAL.VARS = INTERNAL.VARS,
...)
where 11: buildAllPlotsForGene(geneID = geneID, jscs = jscs, outfile.prefix = outfile.prefixes,
use.plotting.device = use.plotting.device, use.vst = use.vst,
use.log = use.log, exon.rescale.factor = exon.rescale.factor,
plot.gene.level.expression = plot.gene.level.expression,
with.TX = with.TX, without.TX = without.TX, expr.plot = expr.plot,
normCounts.plot = normCounts.plot, rExpr.plot = rExpr.plot,
rawCounts.plot = rawCounts.plot, colorRed.FDR.threshold = colorRed.FDR.threshold,
colorList = colorList, plot.exon.results = plot.exon.results,
plot.junction.results = plot.junction.results, plot.novel.junction.results = plot.novel.junction.results,
plot.untestable.results = plot.untestable.results, plot.lwd = plot.lwd,
axes.lwd = axes.lwd, anno.lwd = anno.lwd, gene.lwd = gene.lwd,
drawCoordinates = drawCoordinates, show.strand.arrows = show.strand.arrows,
graph.margins = graph.margins, par.cex = par.cex, anno.cex.text = anno.cex.text,
anno.cex.axis = anno.cex.axis, anno.cex.main = anno.cex.main,
base.plot.height = base.plot.height, base.plot.width = base.plot.width,
base.plot.units = base.plot.units, GENE.annotation.relative.height = GENE.annotation.relative.height,
TX.annotation.relative.height = TX.annotation.relative.height,
CONNECTIONS.relative.height = CONNECTIONS.relative.height,
TX.margins = TX.margins, SPLICE.annotation.relative.height = SPLICE.annotation.relative.height,
autoscale.height.to.fit.TX.annotation = autoscale.height.to.fit.TX.annotation,
autoscale.width.to.fit.bins = autoscale.width.to.fit.bins,
name.files.with.geneID = name.files.with.geneID, plotting.device.params = plotting.device.params,
yAxisLabels.inExponentialForm = yAxisLabels.inExponentialForm,
condition.legend.text = condition.legend.text, include.TX.names = include.TX.names,
draw.start.end.sites = draw.start.end.sites, verbose = verbose,
debug.mode = debug.mode, sequencing.type = sequencing.type,
minimalImageFilenames = minimalImageFilenames, INTERNAL.VARS = INTERNAL.VARS,
...)
where 12: buildAllPlots(jscs)
--- value of length: 3 type: logical ---
[1] FALSE TRUE FALSE
--- function from context ---
function (expr, name, parentenv, handler)
{
.Internal(.addCondHands(name, list(handler), parentenv, environment(),
FALSE))
expr
}
<bytecode: 0x7fdb05496558>
<environment: 0x7fd9f12d4150>
--- function search by body ---
----------- END OF FAILURE REPORT --------------
Fatal error: length > 1 in coercion to logical
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 WARNING, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.11-bioc/meat/JunctionSeq.Rcheck/00check.log’
for details.