8000 Report updates and bugfix by etal · Pull Request #27 · formbio/laava · GitHub
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Report updates and bugfix #27

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Merged
merged 7 commits into from
Jun 11, 2024
Merged

Report updates and bugfix #27

merged 7 commits into from
Jun 11, 2024

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etal
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@etal etal commented Jun 6, 2024 •
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  • Fix Sporadic error in RepCap plot generation #18
  • Update Methods text.
  • Shrink .Rdata by removing unused dataframes and plots.
  • Show "left-/right-snapback" subtype label (per definition table) in length distribution plot when the given vector type is ssAAV.
  • Improve plot aesthetics and make them consistent.

@etal
test/Makefile: recursively clean subdirectories under build/
cdb8e5b 
Report generation can create temporary directories there and leave them
behind if it crashes.
@etal etal force-pushed the report-updates branch 4 times, most recently from cf055a1 to 178cbb5 Compare June 6, 2024 20:03
etal added 4 commits June 6, 2024 16:43
@etal
R: document global options
2564cfe
@etal
calculate_rdata.R: Remove unused dataframes and plots
cf3d18a
@etal
report: Fix repcap plotting error (closes #18)
7703238 
Resolve a ggplot2 deprecation warning about double-dot notation by
replacing `..count..` with `after_stat(count)`.

Split RepCap subsection into separate code blocks for each plot -- each
conditional block only displays one plot.
@etal
report: Update "Methods" text at the end to explain sequence variants.
9e4148f
@etal etal force-pushed the report-updates branch from 178cbb5 to 35ac493 Compare June 6, 2024 23:44
@etal etal requested review from Magdoll and alphabdiallo June 6, 2024 23:44
@etal etal self-assigned this Jun 6, 2024
@etal etal marked this pull request as ready for review June 6, 2024 23:46
alphabdiallo
alphabdiallo approved these changes Jun 8, 2024
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LGMT

etal added 2 commits June 11, 2024 09:44
@etal
calculate_rdata: Show "left/right-snapback" AAV subtype in length dis…
f93f43e 
…t'n plot

When the given vector type is ssAAV, relabel reads assigned the scAAV
type and left- or right-partial subtype to "left-snapback" and
"right-snapback", respectively.

This label is available to downstream consumers in the dataframe column
`x.read.vector$subtype`.
@etal
report: Improve plot aesthetics
5772a8b 
- Set histogram bin width to 150bp, starting from 0.
- Set x- and y-axis origins at 0, where appropriate.
- Where y-axis is the fraction of total reads, in some plots, set its
  max to 1.0 for comparability across reports.
- Use the same "minimal" theme for all plots except the pie chart.
- Use upper-case axis labels instead of title-case, like journals do.
@etal etal force-pushed the report-updates branch from b130bef to 5772a8b Compare June 11, 2024 16:47
@etal etal merged commit d1daea8 into main Jun 11, 2024
3 checks passed
@etal etal deleted the report-updates branch June 11, 2024 17:02
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@alphabdiallo alphabdiallo alphabdiallo approved these changes

@Magdoll Magdoll Awaiting requested review from Magdoll

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Sporadic error in RepCap plot generation
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