Dev #131

jmitchell81 · 2024-07-17T20:35:47Z

dominoSignal v0.99.3

create_domino Function Warnings

Disabled exact p-value computation for the correlation test between receptor expression and features to prevent repeated warning messages due to tied ranks during Spearman correlation calculation

Vignettes

Updated non-functional links to functional URLs
All vignettes explicitly state the seed used when executing their code
The dominoSignal Object vignette states the purpose of the code used to download and import data from a BioFileCache to demonstrate applications of the domino objects on a real data object that is too large to include inside the package

Testing Data

Data used for examples and unit tests is now stored in the package's data/ directory.
All usage of the triple colon operator to access internal data from sysdata have been replaced with usage of data()
Linkage summaries for demonstrating differential linkage testing and plotting are generated within unit test scripts rather than being stored within the package.
Examples are run with echo = FALSE to cut down on lines of code printed in example pages.
Examples for create_domino are run with verbose = FALSE
Fixed example of changing colors for circos_ligand_receptor
Fixed example of boolean representation of cor_heatmap

Dev

fixing broken links and other rmarkdown rendering issues

…b/dominoSignal into testdata_in_pkgdown_yml

The revision to the summarize_linkages function had caused each cell to be assigned to its own cluster. This change perserves the original intention of swapping the cell cluster assignments between the first 120 cells with the second set of 120 cells.

…b/dominoSignal into testdata_in_pkgdown_yml

Testdata in pkgdown yml

Report that regulons will not be stored if tf_targets is not a list as a message. This is to avoid an unessesary warning if someone is running dominoSignal without regulons being considered.

silences the warning for cor.test when their are ambiguous ties in the spearman correlation.

The input argument unit tests were throwing warnings because these tiny objects were not present in the data directory. They had been loaded in by the preceeding code, so the tests did not fail. The data call was removed to prevent the spurious warning.

Usage of example() to generate inputs to function helps test that the whole pipeline is working, but the example pages made by roxygen2 are crowded out by reporting every line of code run. Setting echo to false removes all of these extraneous lines.

Minimize domino create warnings

increased edge weights in signaling plot to appear more clearly on examples. Lowered boolean threshold on cor_heatmap to match build parameters.

The verbose option does not silence text from message() output as part of the example code

The inner arcs of the circos plot could not have altered colors because the names of the clusters were being used on the color vector multiple times on line 39. This ambiguity caused a failure to pick a color when more than one color had the cluster name.

dom_clusters(pbmc_dom_built_tiny) returns a character vector, so the levels function had a NULL result.

dimalvovs

Has been reviewed while merging feature branches to dev and checks pass.

jmitchell81 and others added 30 commits February 5, 2024 13:25

Merge pull request #82 from FertigLab/dev

fdcb941

Dev

removal of pkgdown files

56bba96

update files

c81d091

manual update from master

e95fbba

Merge branch 'master' into bioconductor

94ed4f2

remove pkgdown documentation from master merge

f873189

Merge branch 'master' into bioconductor

9572eba

move data from sysdata.rda to data/

b112ea4

rework examples

a0928b6

rm *_alt and dom_ls_tiny as not needed anymore

e5ccbce

rm tiny_differential_linkage_c2 as it was not used

ca9400e

move differential_linkages from tiny data to examples

8af93ff

fix convenience_fxns tests

8247f1e

move linkage_summary to mock fun

175890b

fully remove mockdata

bf24a0f

bugfix mock_linkage_summary

f8e44b0

fixing broken links and other rmarkdown rendering issues

3a37324

adding ... argument documentation to print method

064f9b8

updating links for reference file and fixing versioning

840d468

Update documentation

8130d79

Merge pull request #127 from FertigLab/krishnan_rmd_fix_134

5bf6447

fixing broken links and other rmarkdown rendering issues

merge pkgdown changes

a561d77

make mocker fun not internal

4c6f1ad

adjust test data for test-import_fxns.R

0b1ec6c

add separate regression tests

ecf48bb

rm the redundant test

36df44a

bump version

cf27467

restore github actions

190b731

restore nojekyll

389578b

restore articles

f0cfd99

jmitchell81 and others added 28 commits July 3, 2024 08:41

Merge branch 'testdata_in_pkgdown_yml' of https://github.com/FertigLa…

edb41c0

…b/dominoSignal into testdata_in_pkgdown_yml

Update documentation

e2db2ab

pkgdown_yml topics for internal test function

e8a3f12

Merge branch 'testdata_in_pkgdown_yml' of https://github.com/FertigLa…

ce95ef3

…b/dominoSignal into testdata_in_pkgdown_yml

dedicated data section in pkgdown references

e515e6e

spelling mistake in issues URL

e42fc50

Update documentation

43d0a34

Update summarize_linkages.Rd

9473fa9

Merge branch 'testdata_in_pkgdown_yml' of https://github.com/FertigLa…

5ccff39

…b/dominoSignal into testdata_in_pkgdown_yml

Merge pull request #129 from FertigLab/testdata_in_pkgdown_yml

2bc835a

Testdata in pkgdown yml

news update for vignettes and testing data

46f5fdb

non-list tf_targets as message

a5ad633

Report that regulons will not be stored if tf_targets is not a list as a message. This is to avoid an unessesary warning if someone is running dominoSignal without regulons being considered.

exact=FALSE cor test

57cf606

silences the warning for cor.test when their are ambiguous ties in the spearman correlation.

Disable example echoes

3463f73

Usage of example() to generate inputs to function helps test that the whole pipeline is working, but the example pages made by roxygen2 are crowded out by reporting every line of code run. Setting echo to false removes all of these extraneous lines.

document silenced examples

2c16ae4

Merge branch 'v0_99_3_news_update' into minimize_domino_create_warnings

2f5adb4

update news

80fb6d4

Merge pull request #130 from FertigLab/minimize_domino_create_warnings

21b358b

Minimize domino create warnings

eexample plot parameters

4497b44

increased edge weights in signaling plot to appear more clearly on examples. Lowered boolean threshold on cor_heatmap to match build parameters.

test example verbose toggle

ff8331f

Update documentation

9fb1ddd

revert verbose false

766eb57

The verbose option does not silence text from message() output as part of the example code

disable verbose create_domino example

7d237ef

circos example colors

35930aa

The inner arcs of the circos plot could not have altered colors because the names of the clusters were being used on the color vector multiple times on line 39. This ambiguity caused a failure to pick a color when more than one color had the cluster name.

do not expect dom_clusters to return a factor

720829a

dom_clusters(pbmc_dom_built_tiny) returns a character vector, so the levels function had a NULL result.

Update NEWS.md

dd974de

dimalvovs approved these changes Jul 18, 2024

View reviewed changes

jmitchell81 merged commit 354dd9f into master Jul 18, 2024
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Dev #131

Dev #131

jmitchell81 commented Jul 17, 2024

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Dev #131

Dev #131

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jmitchell81 commented Jul 17, 2024

dominoSignal v0.99.3

create_domino Function Warnings

Vignettes

Testing Data

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