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address issue with Glimma plots not appearing #99

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address issue with Glimma plots not appearing #99

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1592b07
address issue with Glimma plots not appearing
grimbough Jul 20, 2022
38495e4
Update outdated version number
grimbough Apr 26, 2023
089508a
Fix Copy/paste error
grimbough Apr 26, 2023
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ Title: Standard styles for vignettes and other Bioconductor documents
Description: Provides standard formatting styles for Bioconductor PDF
and HTML documents. Package vignettes illustrate use and
functionality.
Version: 2.25.0
Version: 2.25.1
Authors@R: c(
person("Andrzej", "Oleś", role = "aut",
comment = c(ORCID = "0000-0003-0285-2787")
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9 changes: 9 additions & 0 deletions NEWS
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@@ -1,3 +1,12 @@
CHANGES IN VERSION 2.26.0
------------------------

BUG FIXES

o BiocStyle no longer breaks Javascript inserted by the Glimma package to
produce interactive plots.
(https://github.com/Bioconductor/BiocStyle/issues/97)

CHANGES IN VERSION 2.24.0
------------------------

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10 changes: 8 additions & 2 deletions R/html_document.R
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Expand Up @@ -294,8 +294,14 @@ process_footnotes = function(lines) {
## We wrap tables in a <div> so they can fill the screen on mobile
## but also scroll if they overflow horizontally
process_tables = function(lines) {
lines = gsub("<table", "<div class='horizontal-scroll'><table", lines, fixed = TRUE)
lines = gsub("</table>", "</table></div>", lines, fixed = TRUE)

## this will inadvertantly mess up some javascript e.g. from Glimma
## so we only modify the body of the html
body_start = grep(pattern = "<body>", x = lines, fixed = TRUE)
body_end = grep(pattern = "</body>", x = lines, fixed = TRUE)

lines[body_start:body_start] = gsub("<table", "<div class='horizontal-scroll'><table", lines[body_start:body_start], fixed = TRUE)
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lines[body_start:body_start] = gsub("</table>", "</table></div>", lines[body_start:body_start], fixed = TRUE)
lines
}

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