Update Documentation (concept and input_output) #2

Cecilia-Sensalari · 2021-03-09T13:46:39Z

concept.rst: shortened first section and restructured "explained example"
input_output.rst: completed file lists and descriptions
usage.rst: added path to output filenames to tell where they are generated, peak database description, --n-threads suggestion, description of the multi-page PDF of ortholog Ks distributions

lohausr

See my edits and comments.

doc/source/input_output.rst

doc/source/concept.rst

Co-authored-by: lohausr <56632794+lohausr@users.noreply.github.com>

Cecilia-Sensalari · 2021-03-20T14:49:44Z

Reorganized output files/folders list in input_output.rst
Described ks.tsv file format (added example figure) in input_output.rst
Described ELMM and LMM TSV file format (added example figures) in paralogs_analyses.rst
Replaced the full method descriptions in paralogs_analyses.rst with summaries; referred to the SupMat for the extended explanations. I think that here on the docs it should be more a matter of how to use them and of giving an overview instead of giving detailed and technical descriptions of how they work. Now the page feels also lighter when going through it.

lohausr

A few more edits and comments.

doc/source/concept.rst

lohausr · 2021-03-22T21:33:53Z

doc/source/concept.rst


-.. figure:: _images/ortholog_distribution_peak.svg
+.. figure:: _images/orthologs_distribution_trio.svg


We should remove the medians in the figure once we submit to Bioinformatics.

doc/source/concept.rst

doc/source/input_output.rst

Co-authored-by: lohausr <56632794+lohausr@users.noreply.github.com>

Cecilia-Sensalari · 2021-03-24T16:59:13Z

Tables updated with isopub.txt check and cross symbols
Removed distribution_peak_estimate parameter from expert config files
Applied suggestions in review
Added preprint citation in "How to cite us" page

lohausr

A few more small changes.

doc/source/citation_acknowledgement.rst

lohausr · 2021-03-25T07:26:03Z

doc/source/configuration.rst

@@ -199,7 +198,6 @@ This is an optional configuration file that contains several \"expert\" paramete

 * **logging_level**: the lowest logging/verbosity level of messages printed to the console/logs (increasing severity levels: *notset*, *debug*, *info*, *warning*, *error*, *critical*). Messages less severe than *level* will be ignored; *notset* causes all messages to be processed. [Default: "info"]
 * **max_gene_family_size**: maximum number of members that any paralog gene family can have to be included in *K*:sub:`S` estimation. Large gene families increase the run time and are often composed of unrelated sequences grouped together by shared protein domains or repetitive sequences. But this is not always the case, so one may want to check manually the gene families in file ``paralog_distributions/wgd_<focal species>/<focal species>.mcl.tsv`` and increase (or even decrease) this number. [Default: 200]
-* **distribution_peak_estimate**: the statistical method used to obtain a single ortholog *K*:sub:`S` estimate for the divergence time of a species pair from its ortholog distribution or to obtain a single paralog *K*:sub:`S` estimate from an anchor *K*:sub:`S` cluster or from lognormal components in mixture models (options: "mode" or "median"). [Default: "mode"]


Is this already consistently removed everywhere? Also in the code? Might be a bit early, it's also still in the preprint.

Co-authored-by: lohausr <56632794+lohausr@users.noreply.github.com>

cesen added 3 commits March 9, 2021 14:39

Update documentation (concept.rst)

98daa45

Update Documentation (input_output.rst)

68212ac

Update usage.rst (file paths and descriptions)

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lohausr self-requested a review March 9, 2021 21:50

lohausr requested changes Mar 15, 2021

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Cecilia-Sensalari and others added 7 commits March 17, 2021 11:36

Apply suggestions for concept.rst

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Co-authored-by: lohausr <56632794+lohausr@users.noreply.github.com>

Apply suggestions in input_output.txt

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Co-authored-by: lohausr <56632794+lohausr@users.noreply.github.com>

Apply suggestions in usage.rst

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Merge master into docs

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Update concept.rst

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Merge branch 'master' into docs

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Delete .buildinfo

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Cecilia-Sensalari requested a review from lohausr March 18, 2021 12:54

cesen added 5 commits March 19, 2021 13:49

Describe ks.tsv file format

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Remove "qsub -b y"

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Add (E)LMM file format description; internal links

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Add (E)LMM file figures

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Rename header in ELMM TSV file

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cesen and others added 5 commits March 20, 2021 18:34

Restructure mixture model section and add table

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Reduce paralog analyses description in docs

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Add Note block in input_output.rst about filenames

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Minor change in Note block

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Rename headers in main.nf

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lohausr requested changes Mar 23, 2021

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Cecilia-Sensalari and others added 5 commits March 24, 2021 13:01

Apply suggestions to concept.rst

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Apply suggestions to input_output.rst

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Apply suggestions to usage.rst

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Apply suggestions to paralogs_analyses.rst

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Nextflow header with "ksrates"

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cesen added 7 commits March 24, 2021 17:41

Italics "ksrates" in FAQs header

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Add preprint DOI in "How to cite us" doc page

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Remove "distribution_peak_estimate"

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Update input_output.rst with other suggestions

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Update usage.rst with other suggestions

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Update par_analys.rst with other suggestions

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Update installation.rst with other suggestions

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lohausr requested changes Mar 25, 2021

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Cecilia-Sensalari and others added 3 commits March 25, 2021 09:52

Apply suggestions to How to cite us

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Reintroduce "distribution_peak_estimate" parameter

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Replace <focal species> with species (filename)

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Cecilia-Sensalari merged commit a6e4062 into master Mar 25, 2021

Cecilia-Sensalari deleted the docs branch March 25, 2021 15:56

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Update Documentation (concept and input_output) #2

Update Documentation (concept and input_output) #2

Cecilia-Sensalari commented Mar 9, 2021 •

edited

lohausr left a comment

Cecilia-Sensalari commented Mar 20, 2021 •

edited

lohausr left a comment

lohausr Mar 22, 2021

Cecilia-Sensalari commented Mar 24, 2021

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lohausr Mar 25, 2021


		.. figure:: _images/ortholog_distribution_peak.svg
		.. figure:: _images/orthologs_distribution_trio.svg

Update Documentation (concept and input_output) #2

Update Documentation (concept and input_output) #2

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Cecilia-Sensalari commented Mar 9, 2021 •

edited

Cecilia-Sensalari commented Mar 20, 2021 •

edited