Fix Issue #39: Add ChIP-seq Large Margin Visualization to Gallery

[ANAMASGARD]

Fixes #39
Fixes #35

This PR adds the ChIP-seq large margin visualization AND fixes the title mismatch issue.

1. ChIP-seq Large Margin Viz (Issue #39)

Source Code

• Repo: https://github.com/ANAMASGARD/chip-seq-large-margin-code
• Ported from old animint to animint2 syntax
• Added auto-download for required data files

Deployed Viz

• Repo: https://github.com/ANAMASGARD/chip-seq-large-margin
• Live at: https://ANAMASGARD.github.io/chip-seq-large-margin/
• Deployed with animint2pages() including title and source parameters

Gallery Update

• Added ANAMASGARD/chip-seq-large-margin to repos.txt
• Generated screenshot: repos/ANAMASGARD/chip-seq-large-margin.png

2. Gallery Title Fix (Issue #35)

Fixed title mismatch for climate visualization:

• Before: "Climate change sensor stations"
• After: "CRUTEM4 Temperature Sensor Stations"

The title now matches what's in the source code. Fixed by clearing cached metadata and re-running update_gallery().

Preview

https://ANAMASGARD.github.io/gallery/

@tdhock This is ready for review!

[tdhock]

there are two issues.
old viz below has widerect which is easier to select than the segment you used.

your viz below has blue text too small to read.

please fix. (use widerect, and increase text size)

also why are there so many diff lines in meta.csv?
There should be only 2 because you only modified two gallery entries, right?

[tdhock]

please fix

[ANAMASGARD]

Sir @tdhock,
I’ve addressed your feedback:-

• Made the chip‑seq selection areas wide/easy to click (like widerect).
• Increased the blue explanatory text and sample label sizes so they are readable.

• Cleaned up meta.csv so it only changes the climate title (Issue Mismatch between source titles and gallery titles #35) and adds the chip‑seq entry (Issue chip-seq large margin data viz #39), and regenerated index.html from that.

PLease give your feedback

[tdhock]

rect looks good but blue text still looks too small. it should be about the same size as surrounding text.

[ANAMASGARD]

Sir @tdhock I have increased the size of both the blue text and the black made the size=8 for clear visibility.

• Please review it (Re-Deployed) :- https://anamasgard.github.io/chip-seq-large-margin/

[tdhock]

the text is still too small, can you please increase so that it is same as surrounding text size?

[ANAMASGARD]

Sir @tdhock
Increase the size made it 12 please tell , it is readable without zoom .

[tdhock]

on my screen constant and margin are unreadable (go off of right side of screen). please revise so that they are readable in plotting area.

also the original has smooth transitions: when you change peaks, segment in regression plot updates with a smooth transition. can you please add that?

your viz below only has one peaks selector

original below has a peaks selector for each sample

2 more problems with top plot:

• yours only displays blue peaks for the selected sample (original displays blue peaks for all samples)
• sample names in panel titles overlap

can you please fix?

[ANAMASGARD]

Sir @tdhock, I pushed another update to the ChIP-seq viz :-

• Moved “large margin / small margin / constant” text fully inside the regression panel (no cutoff)
• Added smooth transitions when changing peaks
• Peaks selection is now per-sample (4 selectors)
• Top plot now shows blue peaks for all samples (not only the selected one)
• Fixed the overlapping sample strip titles
  Updated version: https://ANAMASGARD.github.io/chip-seq-large-margin/
  I also updated the gallery screenshot in this PR.
• But McGill0002 sample.ids and blue text they still look small should I increase the size or not ??

Sir review and give your feedback .

[tdhock]

please compare with original. yours looks like this, too many panels

[ANAMASGARD]

Sir @tdhock, I want to explain what happened clearly and ask your preferred next step.

I made a mistake while trying to update the ChIP-seq screenshot/workflow.
I pushed directly to upstream gh-pages, and that caused the PR state to change/merge flow unexpectedly.
Then I reverted those merged changes in commit 5bb862a (Revert PR #46), so the current branch no longer contains the PR #46 content.

• The original work is not deleted from history (commits like 4b1c7ac and related PR Fix Issue #39: Add ChIP-seq Large Margin Visualization to Gallery #46 commits are still visible).
• I understand this caused confusion and extra churn, and I am sorry for that mistake I didn't merged it intentionally i just made all the changes in the
• https://github.com/ANAMASGARD/chip-seq-large-margin-code

Sorry please tell me what should I do now ????

[suhaani-agarwal]

@ANAMASGARD please do not push directly to gh-pages going forward just keep that in mind.
It’s good that you’ve reverted the changes. Please open two separate PRs to address the individual issues (#39 and #35), and please ensure that all previously requested changes are fully incorporated.