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Tp53 figures by broad histology and cancer group #1202

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merged 2 commits into from
Nov 15, 2021
Merged

Tp53 figures by broad histology and cancer group #1202

merged 2 commits into from
Nov 15, 2021

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jharenza
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@jharenza jharenza commented Nov 2, 2021

Purpose/implementation Section

What scientific question is your analysis addressing?

Quick boxplots for TP53 scores by broad histology and cancer group, to align with telomerase scores by cancer group

What was your approach?

Plotted TP53 scores by broad histology or cancer group, removed NAs, and removed Benign, Normal, and Other tumors to align with telomerase cancer group plots

What GitHub issue does your pull request address?

NA

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

NA

Is there anything that you want to discuss further?

No

Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?

Yes

Results

What types of results are included (e.g., table, figure)?

2 figures

What is your summary of the results?

NA

Reproducibility Checklist

  • The dependencies required to run the code in this pull request have been added to the project Dockerfile.
  • This analysis has been added to continuous integration.

Documentation Checklist

  • This analysis module has a README and it is up to date.
  • This analysis is recorded in the table in analyses/README.md and the entry is up to date.
  • The analytical code is documented and contains comments.

jaclyn-taroni
jaclyn-taroni approved these changes Nov 15, 2021
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LGTM. Some notes for what will likely need to change in the future:

I do not see any reason to hold this up for those changes!

@jaclyn-taroni jaclyn-taroni merged commit 4951c98 into AlexsLemonade:master Nov 15, 2021
@jaclyn-taroni jaclyn-taroni mentioned this pull request Nov 17, 2021
Merged
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LauraEgolf added a commit to LauraEgolf/OpenPBTA-analysis that referenced this pull request Jan 5, 2022
@LauraEgolf
Squashed commit of the following:
d310c18 
commit ddb6a8c
Author: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>
Date:   Tue Jan 4 09:33:28 2022 -0500

    OncoPrint figures (AlexsLemonade#1200)

    * Initial pass at histology palette overhaul

    * Add display columns for legends

    * Remove histology label palette NB from CI

    * Add broad histology order

    * Add oncoprint_include

    * Add oncoprint grouping info to palette df

    * Make cancer_group other darker; rerun

    * Pretty sure change in AlexsLemonade#1161 was unintentional

    * We have been manually editing the oncoprint palette I see

    * Remove/move/rename to prep for an oncoprint fig2

    * Missed the instance where I recode based on other hex code

    * Rerun oncoprint now that palette is fixed

    * Change up approach to oncoprint

    * Remove oncoprint script that assembled from PNGs

    * Remove oncoprint PNGs

    * Add new oncoprint figure script

    saves individual panels as PDFs, also uses new palette

    * Add PDFs of oncoprints and legends

    * Add PDF draft of assembled figure 2

    * Update figure shell script

    * Add fig 2 README

    * Add PNG version of draft figure 2

    * Tweak the cancer group palette

    * Reorder HGAT legend; rerun with new palette

    * Remove outdated assembled figure

    * Add compiled versions

    Sizing and spacing probably still need work!

    * Update oncoprint palette

    * Rerun module with new palette

    * Rerun pub ready figure versions of oncoprints

    * Add complex event to oncoprint palette

    * Rerun module with complex event in palette

    * Rerun oncoprint fig script with complex events

    * Darker complex event hex code

    * Try a "wine" color for complex event

    * Remove outdated PNG & PDF of compiled fig

    * Update figures/generate-figures.sh

    Co-authored-by: Chante Bethell  <43576623+cbethell@users.noreply.github.com>

    Co-authored-by: Chante Bethell  <43576623+cbethell@users.noreply.github.com>

commit 32a81d2
Author: runjin326 <47674661+runjin326@users.noreply.github.com>
Date:   Fri Dec 3 17:29:51 2021 -0500

    tables and script added (AlexsLemonade#1199)

    * tables and script added

    * column name changed

    * modified per suggestion + add README

    * tables modified

    * add MB WGS here

    * suggestion implemented and docker file modified

    * re-run on docker

    * dockerfile reverted

    * space removed

    * openxlsx added back to docker

    Co-authored-by: Jo Lynne Rokita <jolynnerokita@d3b.center>
    Co-authored-by: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>

commit 6f3e98c
Author: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>
Date:   Fri Dec 3 08:34:43 2021 -0700

    Revamp `figures` documentation (AlexsLemonade#1209)

    * WIP: figure docs overhaul

    * Polish figures/README.md

    * Add TOC

    * Remove SNV consensus; add breakpoint

    * Update doc to reflect removal of consensus SNV

    * Rearrange table for figure scripts

    * Update figures/README.md

    Co-authored-by: Candace Savonen <cansav09@gmail.com>

    * Update figures/README.md

    Co-authored-by: Candace Savonen <cansav09@gmail.com>

commit c2b5a70
Author: Komal Rathi <komalsrathi@users.noreply.github.com>
Date:   Tue Nov 30 08:42:07 2021 -0500

    add molecular subtype to wgs-only samples (AlexsLemonade#1206)

    Co-authored-by: Jo Lynne Rokita <jolynnerokita@d3b.center>

commit 21d501f
Author: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>
Date:   Sun Nov 28 19:00:41 2021 -0500

    Update interaction plot to use new cancer group palette (AlexsLemonade#1197)

    * Initial pass at histology palette overhaul

    * Add display columns for legends

    * Remove histology label palette NB from CI

    * Add broad histology order

    * Add oncoprint_include

    * Add oncoprint grouping info to palette df

    * Make cancer_group other darker; rerun

    * Save the scatterplot panel as a PDF

    * Add a shell script to run the chromothripsis module

    Also adjust CI accordingly

    * Add session info to R Markdown files

    * Rerun module with changes & commit output

    * Add chromothripsis module to figures script

    * Add figures script for chromothripsis bar plot by cancer group

    * Add Rscript to figures shell script

    Also add the copied version of the other chromothripsis panel

    * Remove lettering from panels

    * Use PDF output for plots with all disease types

    * Add ggpattern to Docker

    * Add patterning to stacked bar chart

    * Move over main interaction figure, now a PDF

    * Missed the instance where I recode based on other hex code

    * Outline the stacked bars in case that's helpful

    * Change up approach to oncoprint

    * Tweak the cancer group palette

    * Remove > 0 filter; rerun with new palette

    * With new cancer group palette, remove the patterns

    * Apply suggestions from code review

    Co-authored-by: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com>

    * Rerun plotting with code changes

    * ggpattern no longer req'd in this branch

    * Remove from script as well

    * Apply suggestions from code review

    Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org>

    Co-authored-by: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com>
    Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org>

commit 2e6cc1b
Author: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>
Date:   Sun Nov 28 17:45:33 2021 -0500

    Update TP53 classifier plots by broad histology and cancer group to fit new conventions (AlexsLemonade#1205)

    * Update tp53 by histology plotting to use new palette; save as PDF

    * Add last plotting script to module shell script

    * Add documentation for recently added script

    * Update variable name

    * Rerun with fix

commit a16bb9d
Author: runjin326 <47674661+runjin326@users.noreply.github.com>
Date:   Sun Nov 28 16:23:01 2021 -0500

    CI calculation added for odds ratio (AlexsLemonade#1204)

    * CI calc added for odds ratio

    * add 0.5 if 0

    * function modified

    * function def

    * rerun and add results

    Co-authored-by: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>

commit 67b555b
Author: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>
Date:   Sun Nov 28 14:21:18 2021 -0500

    Update Figure 4 single panel PDFs, add compiled figure (AlexsLemonade#1194)

    * Initial pass at histology palette overhaul

    * Add display columns for legends

    * Remove histology label palette NB from CI

    * Add broad histology order

    * Add oncoprint_include

    * Add oncoprint grouping info to palette df

    * Allow for alteration of alpha values in custom function

    * Remove immune deconv, rework to use new palette

    * Use updated palette paradigm in telomerase activity box plot

    * Move up telomerase activity plotting so panel can be used downstream

    * Take an approach where individual panels are saved as PDFs

    * panels sub directory

    * Make cancer_group other darker; rerun

    * Rerun telomerase activities

    * Compile individual panels via AI & document

    * Missed the instance where I recode based on other hex code

    * Change up approach to oncoprint

    * Add theme_pubr() to UMAP panel

    * Tweak the cancer group palette

    * Rerun with new cancer group palette

    * Remove outdated assembled figure

    * Updated versions of compiled figure

    * Remove commented out code

commit 6755273
Author: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>
Date:   Sun Nov 28 10:51:18 2021 -0500

    Add Figure 1A component (AlexsLemonade#1195)

    * Add most final component of Fig1 from Biorender

    * Move into panels subdir

commit 0ed1f9b
Author: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>
Date:   Wed Nov 17 15:45:35 2021 -0500

    Update chromothripsis panels to use new cancer group palette (Fig 3) (AlexsLemonade#1196)

    * Initial pass at histology palette overhaul

    * Add display columns for legends

    * Remove histology label palette NB from CI

    * Add broad histology order

    * Add oncoprint_include

    * Add oncoprint grouping info to palette df

    * Make cancer_group other darker; rerun

    * Save the scatterplot panel as a PDF

    * Add a shell script to run the chromothripsis module

    Also adjust CI accordingly

    * Add session info to R Markdown files

    * Rerun module with changes & commit output

    * Add chromothripsis module to figures script

    * Add figures script for chromothripsis bar plot by cancer group

    * Add Rscript to figures shell script

    Also add the copied version of the other chromothripsis panel

    * Missed the instance where I recode based on other hex code

    * Change up approach to oncoprint

    * Tweak the cancer group palette

    * Remove > 0 filter; rerun with new palette

    * Apply suggestions from code review

    Co-authored-by: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com>

    * Rerun plotting with code changes

    Co-authored-by: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com>

commit 5f57826
Author: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>
Date:   Mon Nov 15 16:00:39 2021 -0500

    Create minimal main display item palette (AlexsLemonade#1176) (AlexsLemonade#1193)

    * Initial pass at histology palette overhaul

    * Add display columns for legends

    * Remove histology label palette NB from CI

    * Add broad histology order

    * Add oncoprint_include

    * Add oncoprint grouping info to palette df

    * Make cancer_group other darker; rerun

    * Missed the instance where I recode based on other hex code

    * Change up approach to oncoprint

    * Tweak the cancer group palette

    * Apply suggestions from code review

    Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org>

    * Also display other hex codes with legend()

    Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org>

commit 4951c98
Author: Jo Lynne Rokita <jolynnerokita@d3b.center>
Date:   Mon Nov 15 15:57:33 2021 -0500

    Tp53 figures by broad histology and cancer group (AlexsLemonade#1202)

    * add plots of tp53 scores by histology

    * update path to root

commit 78220da
Author: runjin326 <47674661+runjin326@users.noreply.github.com>
Date:   Fri Oct 22 20:21:18 2021 -0400

    Oncoprint output count tables  (AlexsLemonade#1191)

commit b00d344
Author: Krutika Gaonkar <34580719+kgaonkar6@users.noreply.github.com>
Date:   Sat Oct 23 02:30:22 2021 +0530

    N per cancer_group oncoprint (AlexsLemonade#1189)

    * adding ns per cancer_group

    * add Ns to data outputfolder

    Co-authored-by: kgaonkar6 <gaonkark@chop.edu>
    Co-authored-by: Jo Lynne Rokita <jolynnerokita@d3b.center>

commit 8557352
Author: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>
Date:   Fri Oct 22 14:03:12 2021 -0400

    Take "sufficiently non-zero" approach to exposures for CNS signature fitting (AlexsLemonade#1192)

    * Save & ignore full fit_signatures output

    * Make it easy to just run the CNS fitting part

    * Run all the steps in CI

    * Update analyses/mutational-signatures/run_mutational_signatures.sh

    Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org>

    * Set exposures to zero when lower confidence interval < 0.01

    * Rerun CNS fitting steps

    * Add info about lower interval to README

    Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org>

commit d76ac06
Author: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>
Date:   Thu Oct 21 16:26:51 2021 -0400

    Save output of fit_signatures(), make it easier just to run CNS fitting steps (AlexsLemonade#1190)

    * Save & ignore full fit_signatures output

    * Make it easy to just run the CNS fitting part

    * Run all the steps in CI

    * Update analyses/mutational-signatures/run_mutational_signatures.sh

    Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org>

    Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org>

commit 380b6f1
Author: Jo Lynne Rokita <jolynnerokita@d3b.center>
Date:   Wed Oct 20 15:23:13 2021 -0400

    add Ns and percents to co-occurrence tables for paper (AlexsLemonade#1188)

    * add Ns and percents for paper

    - n_mutated_gene1
    - n_mutated_gene2
    - perc_mutated_gene1
    - perc_mutated_gene2
    - perc_cooccur_or_mutexcl

    * add n_mutated_gene comment

    * clarify `perc_cooccur_or_mutexcl`

    * add all sample percent calculations and update definitions

    clarified to:
    - perc_cooccur_all_samples
    - perc_mutexcl_all_samples
    - perc_cooccur_gene1_mutated
    - perc_mutexcl_gene1_mutated

    * remove ifelse

    * update `perc_cooccur` calculation

    perc_cooccur =  mut11*100/(mut11 + mut10 + mut01)

    * fix typo in perc_mutexcl calculation

    * Update analyses/interaction-plots/scripts/cooccur_functions.R

    Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org>

    * Update analyses/interaction-plots/scripts/cooccur_functions.R

    Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org>

    Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org>
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@jharenza @jaclyn-taroni