ShinyArchR_testPull #1799

rcorces · 2023-01-05T19:23:54Z

test pull request for comparing changes

force create coverage subdirectory within the outputDirectory of the ArchRProject

@exports

also remove @exports from hidden functions

change to safelapply removed variable named "file" also adding return NULL and storing the output of safelapply into a variable to avoid default printing it to std out.

fix mainEmbeds and matrixEmbeds to use the original version of plotEmbedding. Remove all shiny-centric updates to plotEmbedding

make groups apply to both frags and cov

correct function name

is this needed? seems like it should not be needed

fix mainEmbeds and matrixEmbeds to use the original version of plotEmbedding. Remove all shiny-centric updates to plotEmbedding

make groups apply to both frags and cov

correct function name

is this needed? seems like it should not be needed

Revert to native plot embedding

paupaiz and others added 30 commits October 19, 2022 21:26

integrating ShinyArchR to main codebase

14e2c00

Merge branch 'GreenleafLab:dev' into dev

d2b4b21

Merge branch 'GreenleafLab:dev' into dev

e183a1a

modifying after deploying

bef371a

add a @param definition for Shiny loadArchRproj()

a25b9fc

Update AnnotationGenome.R

13ce916

Merge branch 'GreenleafLab:dev' into dev

5844720

Update ArchRBrowser.R

a0ca2d4

adding .validInput to shinyarchr

3ee4410

pattern match to list coverage files

93a5fd9

use previously stored cellGroups

4495ed8

Merge branch 'GreenleafLab:dev' into dev

5e0c9e4

force create coverage

68ea6b0

force create coverage subdirectory within the outputDirectory of the ArchRProject

safelapply to .getGroupFragsFromProj

3a62d51

also remove @exports from hidden functions

cellGroups for consistency

e281685

change cluster to groupIDs

25f39b5

fragFiles

455724f

fix the path to the ArchRProject outputDirectory

c748edf

correct gsub

9e7f165

modify to ShinyRasterUMAPs

0ac8bfe

removing most ArchR::: mine

f5775fc

remove ArchR::: to load hidden functions

3dc3600

downloadFiles()

e57321b

removing all the ArchR:::

bc5431b

adding all files with ArchR:::

09eb384

saving ArchRProjShiny

0bea892

adding arguments to exportShinyArchR

6ec7a17

allow for any embedding in mainUMAPs WIP

fe68765

Merge branch 'GreenleafLab:dev' into dev

0eb9798

"de-hard-coding embeddings"

6306187

paupaiz and others added 30 commits March 26, 2023 22:54

adding stop condition

39622f9

bugfix (file does not exist)

5c27360

change to safelapply removed variable named "file" also adding return NULL and storing the output of safelapply into a variable to avoid default printing it to std out.

return null instead of last result

9351c90

remove Shiny version of plotEmbedding

1325172

fix mainEmbeds and matrixEmbeds to use the original version of plotEmbedding. Remove all shiny-centric updates to plotEmbedding

bugfix

e484d36

bugfix

89fd4af

make groups apply to both frags and cov

add threads argument to exportClusterCoverage

d535380

bugfix addSeqLengths is hidden

bbb2c9f

correct function name

bugfix old arguments

415a8a4

add back feature name storage

0cc7457

remove explicit namespace loading from global

2b1d8fc

is this needed? seems like it should not be needed

bugfix dir name

fc3f673

typo

11039ee

add status reporting for feature plots

e742abb

pass logFile to plotEmbedding

4b37476

Merge branch 'dev' into dev_mrcPlotEmbedding

892080a

typo

ee7e553

remove Shiny version of plotEmbedding

7b1ce6b

fix mainEmbeds and matrixEmbeds to use the original version of plotEmbedding. Remove all shiny-centric updates to plotEmbedding

bugfix

2b577fb

bugfix

3d43d13

make groups apply to both frags and cov

add threads argument to exportClusterCoverage

7872f6a

bugfix addSeqLengths is hidden

18bdc87

correct function name

bugfix old arguments

0139212

add back feature name storage

5d6cb74

remove explicit namespace loading from global

2813105

is this needed? seems like it should not be needed

bugfix dir name

9ad2026

typo

6fb28fd

add status reporting for feature plots

4807128

pass logFile to plotEmbedding

b6b1287

Merge pull request #4 from paupaiz/dev_mrcPlotEmbedding

c970e0e

Revert to native plot embedding

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ShinyArchR_testPull #1799

ShinyArchR_testPull #1799

rcorces commented Jan 5, 2023

ShinyArchR_testPull #1799

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ShinyArchR_testPull #1799

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rcorces commented Jan 5, 2023