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fixed bugs with file lists in index.Rmd
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@jvanheld
jvanheld committed Aug 3, 2018
1 parent f10176e commit b622e3b
Showing 1 changed file with 48 additions and 22 deletions.
70 changes: 48 additions & 22 deletions scripts/RSnakeChunks/R/rna-seq_analysis.R
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Original file line number Diff line number Diff line change
Expand Up @@ -605,7 +605,8 @@ knitr::opts_chunk$set(
figname <- "libsize_barplot_all_features"
file.prefix <- file.path(dir.figures.samples, figname)
message("\t\tGenerating figure\t", figname)
for (fig.format in figure.formats) {
for (f in 1:length(figure.formats)) {
fig.format <- figure.formats[f]
figure.file <- paste(sep = "", file.prefix, ".", fig.format)
figure.files[[fig.format]][figname] <- figure.file
message("\t\t\t", fig.format, " plot\t", figname)
Expand All @@ -614,15 +615,18 @@ knitr::opts_chunk$set(
LibsizeBarplot(counts = all.counts, sample.labels = sample.labels, sample.colors = sample.desc$color, main = "All features", cex.axis = 0.8)

silence <- dev.off(); rm(silence)
index.text <- index.figure(figname, figure.file, index.text)
if (f == 1) {
index.text <- index.figure(figname, figure.file, index.text)
}
# system(paste("open", figure.file))
}


figname <- "libsize_barplot_filtered_features"
file.prefix <- file.path(dir.figures.samples, figname)
message("\t\tGenerating figure\t", figname)
for (fig.format in figure.formats) {
for (f in 1:length(figure.formats)) {
fig.format <- figure.formats[f]
figure.file <- paste(sep = "", file.prefix, ".", fig.format)
figure.files[[fig.format]][figname] <- figure.file
message("\t\t\t", fig.format, " plot\t", figname)
Expand All @@ -631,7 +635,9 @@ knitr::opts_chunk$set(
LibsizeBarplot(counts = filtered.counts, sample.labels = sample.labels, sample.colors = sample.desc$color, main = "After filtering", cex.names = 0.8)

silence <- dev.off(); rm(silence)
index.text <- index.figure(figname, figure.file, index.text)
if (f == 1) {
index.text <- index.figure(figname, figure.file, index.text)
}
# system(paste("open", figure.file))
}

Expand Down Expand Up @@ -663,7 +669,8 @@ knitr::opts_chunk$set(
figname <- "size_factors"
file.prefix <- file.path(dir.figures.samples, figname)
message("\t\tGenerating figure\t", figname)
for (fig.format in figure.formats) {
for (f in 1:length(figure.formats)) {
fig.format <- figure.formats[f]
figure.file <- paste(sep = "", file.prefix, ".", fig.format)
figure.files[[fig.format]][figname] <- figure.file
# message("\t\t\t", fig.format, " plot\t", figname)
Expand All @@ -672,7 +679,9 @@ knitr::opts_chunk$set(
plot(size.factors, main = "Sample size factors", col = sample.desc$color)

silence <- dev.off(); rm(silence)
index.text <- index.figure(figname, figure.file, index.text)
if (f == 1) {
index.text <- index.figure(figname, figure.file, index.text)
}
# system(paste("open", figure.file))
}

Expand Down Expand Up @@ -874,7 +883,8 @@ knitr::opts_chunk$set(
figname <- paste(sep = "", comparison.prefix, "_norm_compa_padj")
file.prefix <- file.path(dir.figures.diffexpr, figname)
message("\t\tGenerating figure\t", figname)
for (fig.format in figure.formats) {
for (f in 1:length(figure.formats)) {
fig.format <- figure.formats[f]
figure.file <- paste(sep = "", file.prefix, ".", fig.format)
figure.files[[fig.format]][figname] <- figure.file
# message("\t\t\t", fig.format, " plot\t", figname)
Expand All @@ -887,14 +897,17 @@ knitr::opts_chunk$set(
main = paste(sep = "", comparison.prefix, "\nAdjusted p-values"))

silence <- dev.off(); rm(silence)
index.text <- index.figure(figname, figure.file, index.text)
if (f == 1) {
index.text <- index.figure(figname, figure.file, index.text)
}
# system(paste("open", figure.file))
}

figname <- paste(sep = "", comparison.prefix, "_norm_compa_log2FC")
file.prefix <- file.path(dir.figures.diffexpr, figname)
message("\t\tGenerating figure\t", figname)
for (fig.format in figure.formats) {
for (f in 1:length(figure.formats)) {
fig.format <- figure.formats[f]
figure.file <- paste(sep = "", file.prefix, ".", fig.format)
figure.files[[fig.format]][figname] <- figure.file
# message("\t\t\t", fig.format, " plot\t", figname)
Expand All @@ -907,7 +920,9 @@ knitr::opts_chunk$set(
main = paste(sep = "", comparison.prefix, "\nlog2(fold change)"))

silence <- dev.off(); rm(silence)
index.text <- index.figure(figname, figure.file, index.text)
if (f == 1) {
index.text <- index.figure(figname, figure.file, index.text)
}
# system(paste("open", figure.file))
}

Expand All @@ -922,7 +937,8 @@ knitr::opts_chunk$set(

file.prefix <- file.path(dir.figures.diffexpr, figname)
message("\t\tGenerating figure\t", figname)
for (fig.format in figure.formats) {
for (f in 1:length(figure.formats)) {
fig.format <- figure.formats[f]
figure.file <- paste(sep = "", file.prefix, ".", fig.format)
figure.files[[fig.format]][figname] <- figure.file
# message("\t\t\t", fig.format, " plot\t", figname)
Expand All @@ -946,7 +962,9 @@ knitr::opts_chunk$set(
par(mfrow = c(1,1))
par(par.ori)
silence <- dev.off(); rm(silence)
index.text <- index.figure(figname, figure.file, index.text)
if (f == 1) {
index.text <- index.figure(figname, figure.file, index.text)
}
# system(paste("open", figure.file))
}

Expand All @@ -963,7 +981,8 @@ knitr::opts_chunk$set(

file.prefix <- file.path(dir.figures.diffexpr, figname)
message("\t\tGenerating figure\t", figname)
for (fig.format in figure.formats) {
for (f in 1:length(figure.formats)) {
fig.format <- figure.formats[f]
figure.file <- paste(sep = "", file.prefix, ".", fig.format)
figure.files[[fig.format]][figname] <- figure.file
# message("\t\t\t", fig.format, " plot\t", figname)
Expand All @@ -989,7 +1008,9 @@ knitr::opts_chunk$set(
par(par.ori)

silence <- dev.off(); rm(silence)
index.text <- index.figure(figname, figure.file, index.text)
if (f == 1) {
index.text <- index.figure(figname, figure.file, index.text)
}
# system(paste("open", figure.file))
}

Expand All @@ -1004,7 +1025,8 @@ knitr::opts_chunk$set(

file.prefix <- file.path(dir.figures.diffexpr, figname)
message("\t\tGenerating figure\t", figname)
for (fig.format in figure.formats) {
for (f in 1:length(figure.formats)) {
fig.format <- figure.formats[f]
figure.file <- paste(sep = "", file.prefix, ".", fig.format)
figure.files[[fig.format]][figname] <- figure.file
# message("\t\t\t", fig.format, " plot\t", figname)
Expand All @@ -1023,7 +1045,9 @@ knitr::opts_chunk$set(
circle.col = c("orange", "blue"), mar = c(0,0,5,0))
}
silence <- dev.off(); rm(silence)
index.text <- index.figure(figname, figure.file, index.text)
if (f == 1) {
index.text <- index.figure(figname, figure.file, index.text)
}
# system(paste("open", figure.file))
}

Expand Down Expand Up @@ -1070,33 +1094,35 @@ knitr::opts_chunk$set(

index.text <- append(index.text, paste(sep = "", "\n\n### Directories\n"))
index.text <- append(index.text, paste(sep = "", "| Content | Path |"))
index.text <- append(index.text, paste(sep = "", "| ---------------------- | -------------------------------------------------- |"))
index.text <- append(index.text, paste(sep = "", "|:----------------------|--------------------------------------------------|"))
for (dirname in names(dirs)) {
dir <- dirs[dirname]
index.text <- append(index.text, paste(sep = "", "| ", dirname, " | ", "[", dir, "](", dir, ") |"))
}

index.text <- append(index.text, paste(sep = "", "\n\n### Input files\n"))
index.text <- append(index.text, paste(sep = "", "| Content | Path |"))
index.text <- append(index.text, paste(sep = "", "| ---------------------- | -------------------------------------------------- |"))
index.text <- append(index.text, paste(sep = "", "|:----------------------|--------------------------------------------------|"))
for (filename in names(infiles)) {
file <- infiles[filename]
index.text <- append(index.text, paste(sep = "", "| ", filename, " | ", "[", file, "](", file, ") |"))
}

index.text <- append(index.text, paste(sep = "", "\n\n### Output files"))
index.text <- append(index.text, paste(sep = "", "| Content | Path |"))
index.text <- append(index.text, paste(sep = "", "| ---------------------- | -------------------------------------------------- |"))
index.text <- append(index.text, paste(sep = "", "|:----------------------|--------------------------------------------------|"))
for (filename in names(outfiles)) {
file <- outfiles[filename]
index.text <- append(index.text, paste(sep = "", "| ", filename, " | ", "[", file, "](", file, ") |"))
}

for (fig.format in names(figure.files)) {
figfiles <- figure.files[fig.format]
f <- 1
for (f in 1:length(figure.formats)) {
fig.format <- figure.formats[f]
figfiles <- unlist(figure.files[fig.format])
index.text <- append(index.text, paste(sep = "", "\n\n### Figures (", fig.format,")"))
index.text <- append(index.text, paste(sep = "", "| Content | Path |"))
index.text <- append(index.text, paste(sep = "", "| ---------------------- | -------------------------------------------------- |"))
index.text <- append(index.text, paste(sep = "", "|----------------------|--------------------------------------------------|"))
for (filename in names(figfiles)) {
file <- figfiles[filename]
index.text <- append(index.text, paste(sep = "", "| ", filename, " | ", "[", file, "](", file, ") |"))
Expand Down

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