Add docx output #302

jashapiro · 2022-08-09T18:18:32Z

Purpose

Modified the github action to build the docx file as well as html and pdf outputs.

Issue

What GitHub issue does your pull request address?

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

In theory this should allow for a .docx output to appear in the output branch, and I would expect to see the same in the artifacts of the build.

Which areas should receive a particularly close look?

How does the output look?

Is there anything that you want to discuss further?

Is the pull request ready for review?

Let's see what happens with the first run.

and trailing spaces, apparently

jashapiro · 2022-08-09T19:05:50Z

Looks like this works, mostly, though the frontmatter is kind of a mess (Word support for SVGs seems... lacking)

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even if we aren't using them

jashapiro · 2022-08-10T20:47:55Z

Marking this ready for review. I replaced the icon svgs with pngs, which solved the awful docx rendering, at the cost of slightly less pretty pdf & html output.

Otherwise, the docx rendering looks fine, and I added it to the appveyor script for one-click download of the docx version (e.g. #302 (comment)).

I believe that the github action update means the output branch will get the docx file on merge as well, but somebody might want to confirm that.

content/06.methods.md

https://link.springer.com/article/10.1007/s00381-017-3481-3

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jashapiro

Noting below which lines in the methods are not just whitespace changes

jashapiro · 2022-08-10T23:37:43Z

content/06.methods.md

@@ -292,7 +292,7 @@ Based on pediatric cancer literature review, we added _MYBL1_ [@doi:10.1073/pnas
 #### Oncoprint figure generation (`oncoprint-landscape` analysis module)

 We used `Maftools` [@doi:10.1101/gr.239244.118] to generate oncoprints depicting the frequencies of canonical somatic gene mutations, CNVs, and fusions for the top 20 genes mutated across primary tumors within broad histologies of the OpenPBTA dataset.
-We collated canonical genes from the literature for low-grade astrocytic tumors [@doi:10.1186/s40478-020-00902-z], embryonal tumors [@doi:10.1038/nature22973; @doi:10.1007/s00401-020-02182-2; @doi:10.1186/s40478-020-00984-9; @doi:10.1016/j.ccell.2016.02.001; @doi:10.1038/s41598-020-59812-8], diffuse astrocytic and oligodendroglial tumors [@doi:10.1016/j.ccell.2017.08.017; @doi:10.1002/ijc.32258; @doi:10.1093/neuonc/noab106; @doi:10.1186/s40478-020-00905-w],  and other tumors: ependymal tumors, craniopharyngiomas, neuronal-glial mixed tumors, histiocytic tumors, chordoma, meningioma, and choroid plexus tumors [@doi:10.1007/s00381-017-3481-3; @doi:10.1016/j.ccell.2015.04.002; @doi:10.1038/nature13109; @doi:10.1038/s41525-017-0014-7; @doi:10.3171/2019.8.JNS191266; @doi:10.1007/s00401-016-1539-z; @doi:10.1093/neuonc/noaa267; @doi:10.1016/s0002-9440(10)64477-x; @doi:10.1016/j.jaad.2017.05.059; @doi:10.1186/s40478-020-01056-8].
+We collated canonical genes from the literature for low-grade astrocytic tumors [@doi:10.1186/s40478-020-00902-z], embryonal tumors [@doi:10.1038/nature22973; @doi:10.1007/s00401-020-02182-2; @doi:10.1186/s40478-020-00984-9; @doi:10.1016/j.ccell.2016.02.001; @doi:10.1038/s41598-020-59812-8], diffuse astrocytic and oligodendroglial tumors [@doi:10.1016/j.ccell.2017.08.017; @doi:10.1002/ijc.32258; @doi:10.1093/neuonc/noab106; @doi:10.1186/s40478-020-00905-w],  and other tumors: ependymal tumors, craniopharyngiomas, neuronal-glial mixed tumors, histiocytic tumors, chordoma, meningioma, and choroid plexus tumors [@pmid:28623522; @doi:10.1016/j.ccell.2015.04.002; @doi:10.1038/nature13109; @doi:10.1038/s41525-017-0014-7; @doi:10.3171/2019.8.JNS191266; @doi:10.1007/s00401-016-1539-z; @doi:10.1093/neuonc/noaa267; @pmid:12466115; @doi:10.1016/j.jaad.2017.05.059; @doi:10.1186/s40478-020-01056-8].


Non-whitespace change

jashapiro · 2022-08-10T23:38:20Z

content/06.methods.md

-We predicted telomerase activity of tumor samples using the recently developed `EXTEND` method [@doi:https://doi.org/10.1101/2020.05.21.109249].
-Briefly, `EXTEND` estimates telomerase activity based on the expression of a 13-gene signature. 
-We derived this signature by comparing telomerase-positive tumors and tumors with activated alternative lengthening of telomeres pathway, a group presumably negative of telomerase activity. 
+We predicted telomerase activity of tumor samples using the recently developed `EXTEND` method [@doi:10.1038/s41467-020-20474-9].


Updated reference (now published!)

jashapiro · 2022-08-10T23:40:21Z

content/06.methods.md


 ### Survival models (`survival-analysis` analysis module)

 We calculated overall survival (OS) as days since initial diagnosis and performed several survival analyses on the OpenPBTA cohort using the [`survival` R package](https://cran.r-project.org/package=survival).
 We performed survival analysis for patients by HGG subtype using the Kaplan-Meier estimator [@doi:10.2307/2281868] and a log-rank test (Mantel-Cox test) [@pmid:5910392] on the different HGG subtypes.
-Next, we used multivariate cox (proportional hazards) regression analysis [@url:http://www.jstor.org/stable/2985181] to model the following: a) `tp53 scores + telomerase scores + extent of tumor resection + LGG group + HGG group`, in which `tp53 scores` and `telomerase scores` are numeric, `extent of tumor resection` is categorical, and `LGG group` and `HGG group` are binary variables indicating whether the sample is in either broad histology grouping, b) `tp53 scores + telomerase scores + extent of tumor resection` for each `cancer_group` with an N>=3 deceased patients (DIPG, DMG, HGG, MB, and EPN), and c) `quantiseq cell type fractions + CD274 expression + extent of tumor resection` for each `cancer_group` with an N>=3 deceased patients (DIPG, DMG, HGG, MB, and EPN), in which `quantiseq cell type fractions` and `CD274 expression` are numeric.
+Next, we used multivariate Cox (proportional hazards) regression analysis [@doi:10.1111/j.2517-6161.1972.tb00899.x] to model the following: a) `tp53 scores + telomerase scores + extent of tumor resection + LGG group + HGG group`, in which `tp53 scores` and `telomerase scores` are numeric, `extent of tumor resection` is categorical, and `LGG group` and `HGG group` are binary variables indicating whether the sample is in either broad histology grouping, b) `tp53 scores + telomerase scores + extent of tumor resection` for each `cancer_group` with an N>=3 deceased patients (DIPG, DMG, HGG, MB, and EPN), and c) `quantiseq cell type fractions + CD274 expression + extent of tumor resection` for each `cancer_group` with an N>=3 deceased patients (DIPG, DMG, HGG, MB, and EPN), in which `quantiseq cell type fractions` and `CD274 expression` are numeric.


Found DOI for this ref.

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jharenza

This looks good, and no more ???!

jharenza · 2022-08-11T00:04:22Z

The one thing I noticed and wanted to note somewhere is that the reference format is general Manubot format and I am wondering if there will be a way to make the references in the output journal-specific. I can add a new ticket around this, as I think we do not need to address immediately nor prior to sending to co-authors.

jharenza · 2022-08-11T00:11:03Z

Update: created #304 for reference style.

jaclyn-taroni

🚀

[ci skip] This build is based on 42246c7. This commit was created by the following CI build and job: https://github.com/AlexsLemonade/OpenPBTA-manuscript/commit/42246c7e0dcc3916476ffca2a5f51b9e03b10768/checks https://github.com/AlexsLemonade/OpenPBTA-manuscript/runs/2841612758

jashapiro added 2 commits August 9, 2022 14:12

Add docx output

e912d43

attempt doi fixes

7a5276f

and trailing spaces, apparently

Merge remote-tracking branch 'upstream/master' into jashapiro/docx-up…

1fa3e92

…date

try pngs

52a46a0

jashapiro added 2 commits August 10, 2022 16:10

use the pngs

0a4f41f

Add docx to appveyor

e6a858a

jashapiro marked this pull request as ready for review August 10, 2022 20:41

put the svgs back

0490476

even if we aren't using them

jashapiro commented Aug 10, 2022

View reviewed changes

content/06.methods.md Outdated Show resolved Hide resolved

jashapiro added 2 commits August 10, 2022 16:52

Annother attempt at Ryall et al. ref

8eb1557

https://link.springer.com/article/10.1007/s00381-017-3481-3

try pubmed id

64f6ac7

jashapiro added 4 commits August 10, 2022 17:34

update EXTEND doi

a5e07a3

update fig reference

06e0b91

Fix doi with parens & others

530ab9c

doi for Cox 1972

1c483c9

jashapiro requested review from jaclyn-taroni and jharenza August 10, 2022 23:36

capitalize Cox

8050704

jashapiro commented Aug 10, 2022

View reviewed changes

jharenza approved these changes Aug 11, 2022

View reviewed changes

jaclyn-taroni approved these changes Aug 11, 2022

View reviewed changes

jashapiro merged commit 42246c7 into AlexsLemonade:master Aug 11, 2022

jashapiro deleted the jashapiro/docx-update branch August 11, 2022 17:22

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Add docx output #302

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Add docx output #302

Add docx output #302

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jashapiro commented Aug 9, 2022

Purpose

Issue

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

Which areas should receive a particularly close look?

Is there anything that you want to discuss further?

Is the pull request ready for review?

jashapiro commented Aug 9, 2022

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