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fix(plotting): Fix groupComparisonPlots to render when viewport dims are low #206

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Merged
tonywu1999 merged 1 commit into from
Apr 29, 2026
Merged

fix(plotting): Fix groupComparisonPlots to render when viewport dims are low #206

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4 changes: 3 additions & 1 deletion .Rbuildignore
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Original file line number Diff line number Diff line change
Expand Up @@ -5,4 +5,6 @@
^_pkgdown\.yml$
^docs$
^pkgdown$
appspec.yml
appspec.yml
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@coderabbitai coderabbitai Bot Apr 29, 2026

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⚠️ Potential issue | 🟡 Minor

🧩 Analysis chain

🏁 Script executed:

#!/bin/bash
# Check the previous format of the appspec.yml pattern
git log -p --follow -S "appspec" -- .Rbuildignore | head -30

Repository: Vitek-Lab/MSstats

Length of output: 43

🏁 Script executed:

cat -n .Rbuildignore

Repository: Vitek-Lab/MSstats

Length of output: 258

Ensure pattern consistency for .Rbuildignore entries.

The appspec.yml pattern on line 8 lacks regex anchors, making it inconsistent with all other entries in the file. Every other pattern uses the ^ prefix (and many use trailing $ as well), including the newly added ^\.positai$ and ^\.claude$ on lines 9-10. The unanchored pattern appspec.yml will match the filename anywhere in the path, whereas the anchored patterns match only at the root.

Consider changing it to ^appspec\.yml$ to match the format of surrounding entries.

🤖 Prompt for AI Agents 
Verify each finding against the current code and only fix it if needed.

In @.Rbuildignore at line 8, Update the .Rbuildignore entry for the appspec file
to use anchored regex like the surrounding entries: replace the unanchored
literal "appspec.yml" with a pattern such as "^appspec\\.yml$" so it matches
only the root filename and remains consistent with entries like "^\\.positai$"
and "^\\.claude$"; edit the existing appspec.yml line accordingly.

^\.positai$
^\.claude$
1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -9,3 +9,4 @@
.idea
*.Rproj

.positai
4 changes: 2 additions & 2 deletions R/groupComparisonPlots.R
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Original file line number Diff line number Diff line change
Expand Up @@ -369,7 +369,7 @@ groupComparisonPlots = function(
plot = .makeVolcano(single_label, label_name, log_base_FC, log_base_pval, x.lim, ProteinName, dot.size,
y.limdown, y.limup, text.size, FCcutoff, sig, x.axis.size, y.axis.size,
legend.size, log_adjp)
print(plot)
if (!isPlotly) print(plot)
plots[[i]] = plot
}
if (address != FALSE) {
Expand Down Expand Up @@ -423,7 +423,7 @@ groupComparisonPlots = function(
plot = .makeComparison(single_protein, log_base_FC, dot.size, x.axis.size,
y.axis.size, text.angle, hjust, vjust, y.limdown,
y.limup, sig)
print(plot)
if (!isPlotly) print(plot)
plots[[i]] = plot
}
if (address != FALSE) {
Expand Down
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