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Numbered PNG plots working as output, with related refactor. Sample s…
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…etup screen in place.
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@Jakob37
Jakob37 committed Jun 2, 2020
1 parent 18cdacf commit 5e2f7ec
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179 changes: 48 additions & 131 deletions R/generatePlots.R
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Original file line number Diff line number Diff line change
Expand Up @@ -103,7 +103,7 @@
#' normResultsWithEval <- analyzeNormalizations(normResults)
#' outputDir <- tempdir()
#' generatePlots(normResultsWithEval, outputDir)
generatePlots <- function(nr, jobdir, plotRows=3, plotCols=4, writeAsPngs=FALSE) {
generatePlots <- function(nr, jobdir, plotRows=3, plotCols=4, writeAsPngs=TRUE) {

nds <- nds(nr)
currentjob <- jobName(nds)
Expand All @@ -118,146 +118,65 @@ generatePlots <- function(nr, jobdir, plotRows=3, plotCols=4, writeAsPngs=FALSE)
default.units=c('null', 'null')
)

pageno <- 1
nextPageNo <- function(iter=TRUE) {
if (iter) {
pageno <<- pageno + 1
}
pageno
}

currentFont <- "Helvetica"
setupPlotting(currentjob, jobdir, "Norm-report")

# function(outputFunc, jobdir, pngPath=NULL, ...) {

# pngDir <- sprintf("%s/pngs", jobdir)
# dir.create(pngDir)
pngDir <- sprintf("%s/pngs", jobdir)

# writePage(plotFrontPage, jobdir, sprintf("%s/%s", pngDir, "front_page.png"), currentjob, currentFont)
plotFrontPage(currentjob, currentFont)

# writePage
#
# if (!writeAsPngs) {
# }
# else {
#
# png(filename=sprintf("%s/pngs/1_FrontPage.png", jobdir))
# plotFrontPage(currentjob, currentFont)
# dev.off()
# }
if (writeAsPngs) {
dir.create(pngDir)
}

writePage(plotFrontPage, jobdir, writeAsPngs, sprintf("%s/%s_%s", pngDir, nextPageNo(iter=FALSE), "front_page.png"), currentjob, currentFont)
isLimitedRun <- singleReplicateRun(nds) || isTinyRun(nds)

# Sample mapping
pageno <- 2
# writePage(plotSampleMappingPage, jobdir, sprintf("%s/%s", pngDir, "sample_map.png"), nr, currentFont, pageno)
plotSampleMappingPage(nr, currentFont, currentLayout, currentjob, pageno)
# png(filename = "~/Desktop/A.png")
# dev.off()

# TI
pageno <- pageno + 1
# png(filename = "~/Desktop/B.png")
plotSampleOutlierSummary(nr, currentLayout, pageno)
# dev.off()

writePage(plotSampleMappingPage, jobdir, writeAsPngs, sprintf("%s/%s_%s", pngDir, nextPageNo(iter=TRUE), "sample_setup.png"), nr, currentFont, currentLayout, currentjob, nextPageNo(iter=FALSE))
writePage(plotSampleOutlierSummary, jobdir, writeAsPngs, sprintf("%s/%s_%s", pngDir, nextPageNo(iter=TRUE), "outlier_detection.png"), nr, currentLayout, nextPageNo(iter=FALSE))

# If running with single-replicates, skip replicate dependent quality plots
if (!isLimitedRun) {
# CV
pageno <- pageno + 1
# png(filename = "~/Desktop/C.png")
plotReplicateVariance(nr, currentLayout, pageno)
# dev.off()

# Stable variables plot and CV in percent difference
pageno <- pageno + 1
# png(filename = "~/Desktop/D.png")
plotReplicateVarAndStableVariables(nr, currentLayout, pageno)
# dev.off()

# CVvsintensityplot
pageno <- pageno + 1
# png(filename = "~/Desktop/E.png")
plotCVvsIntensity(nr, currentLayout, pageno)
# dev.off()

# MA plots
pageno <- pageno + 1
# png(filename = "~/Desktop/F.png")
plotMA(nr, currentLayout, pageno)
# dev.off()
writePage(plotReplicateVariance, jobdir, writeAsPngs, sprintf("%s/%s_%s", pngDir, nextPageNo(iter=TRUE), "replicate_variation.png"), nr, currentLayout, nextPageNo(iter=FALSE))
writePage(plotReplicateVarAndStableVariables, jobdir, writeAsPngs, sprintf("%s/%s_%s", pngDir, nextPageNo(iter=TRUE), "replicate_variation_rel_to_log2.png"), nr, currentLayout, nextPageNo(iter=FALSE))
writePage(plotCVvsIntensity, jobdir, writeAsPngs, sprintf("%s/%s_%s", pngDir, nextPageNo(iter=TRUE), "cv_vs_raw_intensity.png"), nr, currentLayout, nextPageNo(iter=FALSE))
writePage(plotMA, jobdir, writeAsPngs, sprintf("%s/%s_%s", pngDir, nextPageNo(iter=TRUE), "ma.png"), nr, currentLayout, nextPageNo(iter=FALSE))
}

# Scatterplots
pageno <- pageno + 1
# png(filename = "~/Desktop/G.png")
plotScatter(nr, currentLayout, pageno)
# dev.off()

# QQplot
pageno <- pageno + 1
# png(filename = "~/Desktop/H.png")
plotQQ(nr, currentLayout, pageno)
# dev.off()

# Boxplot
pageno <- pageno + 1
# png(filename = "~/Desktop/I.png")
plotBoxPlot(nr, currentLayout, pageno)
# dev.off()

# RLE plots
pageno <- pageno + 1
# png(filename = "~/Desktop/J.png")
plotRLE(nr, currentLayout, pageno)
# dev.off()

# Density plots
pageno <- pageno + 1
# png(filename = "~/Desktop/K.png")
plotDensity(nr, currentLayout, pageno)
# dev.off()

# MDS plot
pageno <- pageno + 1
# png(filename = "~/Desktop/L.png")
plotMDS(nr, currentLayout, pageno)
# dev.off()

writePage(plotScatter, jobdir, writeAsPngs, sprintf("%s/%s_%s", pngDir, nextPageNo(iter=TRUE), "scatter.png"), nr, currentLayout, nextPageNo(iter=FALSE))
writePage(plotQQ, jobdir, writeAsPngs, sprintf("%s/%s_%s", pngDir, nextPageNo(iter=TRUE), "qqplots.png"), nr, currentLayout, nextPageNo(iter=FALSE))
writePage(plotBoxPlot, jobdir, writeAsPngs, sprintf("%s/%s_%s", pngDir, nextPageNo(iter=TRUE), "boxplot.png"), nr, currentLayout, nextPageNo(iter=FALSE))
writePage(plotRLE, jobdir, writeAsPngs, sprintf("%s/%s_%s", pngDir, nextPageNo(iter=TRUE), "rel_log_expr.png"), nr, currentLayout, nextPageNo(iter=FALSE))
writePage(plotDensity, jobdir, writeAsPngs, sprintf("%s/%s_%s", pngDir, nextPageNo(iter=TRUE), "density.png"), nr, currentLayout, nextPageNo(iter=FALSE))
writePage(plotMDS, jobdir, writeAsPngs, sprintf("%s/%s_%s", pngDir, nextPageNo(iter=TRUE), "mds.png"), nr, currentLayout, nextPageNo(iter=FALSE))

if (!isLimitedRun) {

# meanSDplot
pageno <- pageno + 1
# png(filename = "~/Desktop/M.png")
plotMeanSD(nr, currentLayout, pageno)
# dev.off()

# Correlation
pageno <- pageno + 1
# png(filename = "~/Desktop/N.png")
plotCorrelation(nr, currentLayout, pageno)
# dev.off()
writePage(plotMeanSD, jobdir, writeAsPngs, sprintf("%s/%s_%s", pngDir, nextPageNo(iter=TRUE), "mean_sd.png"), nr, currentLayout, nextPageNo(iter=FALSE))
writePage(plotCorrelation, jobdir, writeAsPngs, sprintf("%s/%s_%s", pngDir, nextPageNo(iter=TRUE), "correlation.png"), nr, currentLayout, nextPageNo(iter=FALSE))
}

# Dendrograms
pageno <- pageno + 1
# png(filename = "~/Desktop/O.png")
plotDendrograms(nr, currentLayout, pageno)
# dev.off()

writePage(plotDendrograms, jobdir, writeAsPngs, sprintf("%s/%s_%s", pngDir, nextPageNo(iter=TRUE), "dendrogram.png"), nr, currentLayout, nextPageNo(iter=FALSE))

if (!isLimitedRun) {
# DE plots
pageno <- pageno + 1
# png(filename = "~/Desktop/P.png")
plotPHist(nr, currentLayout, pageno)
# dev.off()
writePage(plotPHist, jobdir, writeAsPngs, sprintf("%s/%s_%s", pngDir, nextPageNo(iter=TRUE), "sample_setup.png"), nr, currentLayout, nextPageNo(iter=FALSE))
}

grDevices::dev.off()
}

writePage <- function(outputFunc, jobdir, pngPath=NULL, ...) {
if (is.null(pngPath)) {
writePage <- function(outputFunc, jobdir, writeAsPngs, pngPath=NULL, ...) {
if (!is.null(pngPath) && writeAsPngs) {
png(filename=pngPath, width = 11.7, height = 8.3, units="in", res=300)
outputFunc(...)
dev.off()
}
else {
png(filename=pngPath, width = 11.7, height = 8.3, units="in", res=300)
outputFunc(...)
dev.off()
}
}

Expand Down Expand Up @@ -291,7 +210,7 @@ setupPlotting <- function(currentJob, jobDir, suffix) {
plot.title=ggplot2::element_text(size=8),
plot.margin=ggplot2::unit(c(1, 1, 1, 1), "mm")
)
def.par <- graphics::par(no.readonly=TRUE)
# def.par <- graphics::par(no.readonly=TRUE)
}

#' Generate first page in output report and write to viewport
Expand Down Expand Up @@ -381,9 +300,6 @@ plotFrontPage <- function(currentjob, currentFont) {
plotSampleMappingPage <- function(nr, currentFont, currentLayout, currentjob, pageno) {

nds <- nds(nr)
methodlist <- normalizations(nr)
filterED <- sampleReplicateGroups(nds)
filterrawdata <- filterrawdata(nds)
currentjob <- jobName(nds)

tout <- rbind(c(1, 2), c(3, 4))
Expand All @@ -397,27 +313,28 @@ plotSampleMappingPage <- function(nr, currentFont, currentLayout, currentjob, pa
groupLevels <- levels(as.factor(groupCol))
condCounts <- table(groupCol)

groupStrings <- lapply(
groupList <- lapply(
1:length(groupLevels),
function(lv, groups, groupCounts) {
sprintf("%s\t%s\t%s", lv, groups[[lv]], groupCounts[[lv]]) },
list(groupNbr=lv, groupString=groups[[lv]], groupCount=groupCounts[[lv]])
},
groups=groupLevels, groupCounts=condCounts)

groupStringsWHead <- c("group\tlevel\tcount", "", groupStrings)
groupStringsWHead <- c(list(list(groupNbr="Group nbr.", groupString="Design group", groupCount="Nbr. samples in cond."), list(groupNbr="", groupString="", groupCount="")), groupList)

lapply(1:length(groupStringsWHead), function(i, stringsToShow) {
grid::grid.text(stringsToShow[[i]], x=0.01, y=0.9-i*0.02, hjust=0)
yPos <- 0.9-i*0.02
xDelta <- 0.15
grid::grid.text(stringsToShow[[i]]$groupNbr, x=0.01, y=yPos, hjust=0)
grid::grid.text(stringsToShow[[i]]$groupString, x=0.01+xDelta, y=yPos, hjust=0)
grid::grid.text(stringsToShow[[i]]$groupCount, x=0.01+2*xDelta, y=yPos, hjust=0)
}, groupStringsWHead)

grid::grid.text(
"Please note that the grouping only impacts evaluation measures and visuals seen here, it does not have any impact on the performed normalizations.",
"Please note that the grouping only impacts evaluation measures and visuals seen in the report, they do not impact the performed normalizations.",
x=0.01, y=0.1, hjust=0
)


#
# gp <- grid::gpar(fontsize=11, fontfamily="Helvetica",
# col="black", fontface="bold")
grid::pushViewport(grid::viewport(layout=currentLayout))
printMeta(
"Sample setup",
Expand Down
2 changes: 1 addition & 1 deletion R/printMeta.R
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@ printMeta <- function(plotname, pageno, jobname, currentLayout) {
vp=grid::viewport(layout.pos.row=1, layout.pos.col=1),
just=c("left", "center"),
gp=grid::gpar(fontface="bold", fontsize=14, fontfamily="Helvetica", col="darkBlue"))
grid::grid.text("Normalyzer Report",
grid::grid.text("NormalyzerDE Report",
vp=grid::viewport(layout.pos.row=1, layout.pos.col=ncol),
just=c("right", "center"), gp=gp)
grid::grid.text(paste("Page ", pageno,sep=""),
Expand Down

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