loomr.git
19 months agoset stringsAsFactors = FALSE in get.attribute.df
Christoph Hafemeister [Wed, 21 Mar 2018 21:51:12 +0000 (22:51 +0100)]
set stringsAsFactors = FALSE in get.attribute.df

19 months agoModify get.attribute.df to return all attributes by default and to skip all 2D attributes
Christoph Hafemeister [Wed, 21 Mar 2018 21:37:27 +0000 (22:37 +0100)]
Modify get.attribute.df to return all attributes by default and to skip all 2D attributes

19 months agoHave create, combine, and subset.loom automatically create graph groups instead of...
Paul Hoffman [Wed, 21 Mar 2018 19:33:01 +0000 (15:33 -0400)]
Have create, combine, and subset.loom automatically create graph groups instead of edge groups

19 months agoAdd validation for graphs
Paul Hoffman [Wed, 21 Mar 2018 19:28:19 +0000 (15:28 -0400)]
Add validation for graphs

19 months agoRemove redundant code
Paul Hoffman [Wed, 21 Mar 2018 18:15:55 +0000 (14:15 -0400)]
Remove redundant code

19 months agoBug fix in subset.loom
Paul Hoffman [Tue, 20 Mar 2018 22:51:27 +0000 (18:51 -0400)]
Bug fix in subset.loom

20 months agoFixes to apply, field loading, and subset.loom; new update.shape method
Paul Hoffman [Mon, 19 Mar 2018 20:50:33 +0000 (16:50 -0400)]
Fixes to apply, field loading, and subset.loom; new update.shape method

20 months agoChanges to warning messages in create
Paul Hoffman [Mon, 19 Mar 2018 15:33:45 +0000 (11:33 -0400)]
Changes to warning messages in create

20 months agoProvide S4 Matrix methods to loomR for data manipulation
Paul Hoffman [Mon, 19 Mar 2018 14:42:43 +0000 (10:42 -0400)]
Provide S4 Matrix methods to loomR for data manipulation

20 months agoFixes to loom$apply and subset.loom
Paul Hoffman [Fri, 16 Mar 2018 23:18:31 +0000 (19:18 -0400)]
Fixes to loom$apply and subset.loom

20 months agoMinor fix in loom
Paul Hoffman [Fri, 16 Mar 2018 20:29:24 +0000 (16:29 -0400)]
Minor fix in loom

20 months agoUpdate documentation, change the way apply creates datasets
Paul Hoffman [Thu, 15 Mar 2018 15:09:01 +0000 (11:09 -0400)]
Update documentation, change the way apply creates datasets

20 months agoUpdate documentation
Paul Hoffman [Wed, 14 Mar 2018 17:55:46 +0000 (13:55 -0400)]
Update documentation

20 months agoShow link for subset.loom when calling help on subset
Paul Hoffman [Wed, 14 Mar 2018 17:55:38 +0000 (13:55 -0400)]
Show link for subset.loom when calling help on subset

20 months agoTweaks to catn
Paul Hoffman [Wed, 14 Mar 2018 17:55:04 +0000 (13:55 -0400)]
Tweaks to catn

20 months agoAdd ability to transpose input data
Paul Hoffman [Thu, 8 Mar 2018 23:54:07 +0000 (18:54 -0500)]
Add ability to transpose input data

20 months agoUpdate README
Paul Hoffman [Thu, 8 Mar 2018 23:53:54 +0000 (18:53 -0500)]
Update README

20 months agoMerge branch 'master' into develop
Paul Hoffman [Mon, 5 Mar 2018 23:03:49 +0000 (18:03 -0500)]
Merge branch 'master' into develop

20 months agoAdd loomR::combine
Paul Hoffman [Thu, 1 Mar 2018 00:35:51 +0000 (19:35 -0500)]
Add loomR::combine

20 months agoUpate documentation
Paul Hoffman [Thu, 1 Mar 2018 00:35:37 +0000 (19:35 -0500)]
Upate documentation

20 months agoMore updates
Paul Hoffman [Wed, 28 Feb 2018 23:22:18 +0000 (18:22 -0500)]
More updates

20 months agoUpdates to gitignore and DESCRIPTION
Paul Hoffman [Wed, 28 Feb 2018 16:14:31 +0000 (11:14 -0500)]
Updates to gitignore and DESCRIPTION

20 months agoMerge branch 'develop' of github.com:mojaveazure/loomR into develop
Paul Hoffman [Tue, 27 Feb 2018 23:50:20 +0000 (18:50 -0500)]
Merge branch 'develop' of github.com:mojaveazure/loomR into develop

20 months agoStart working on a combine function
Paul Hoffman [Tue, 27 Feb 2018 23:50:10 +0000 (18:50 -0500)]
Start working on a combine function

20 months agoMinor usability fix
Paul Hoffman [Fri, 23 Feb 2018 23:49:39 +0000 (18:49 -0500)]
Minor usability fix

20 months agoMerge branch 'develop' of github.com:mojaveazure/loomR into develop
Andrew Butler [Fri, 23 Feb 2018 19:46:08 +0000 (14:46 -0500)]
Merge branch 'develop' of github.com:mojaveazure/loomR into develop

20 months agoclose progress bar connections
Andrew Butler [Fri, 23 Feb 2018 19:45:43 +0000 (14:45 -0500)]
close progress bar connections

20 months agoChange validation to add missing groups; update documentation
Paul Hoffman [Thu, 22 Feb 2018 23:21:43 +0000 (18:21 -0500)]
Change validation to add missing groups; update documentation

20 months agoAdd preliminary support for row and column edges
Paul Hoffman [Wed, 21 Feb 2018 23:24:09 +0000 (18:24 -0500)]
Add preliminary support for row and column edges

21 months agoallow add.attribute to take a data.frame - convert to named list
andrewwbutler [Fri, 9 Feb 2018 19:43:20 +0000 (14:43 -0500)]
allow add.attribute to take a data.frame - convert to named list

21 months agoUpdate documentation some more
Paul Hoffman [Fri, 9 Feb 2018 03:12:25 +0000 (22:12 -0500)]
Update documentation some more

21 months agoUpdate documentation
Paul Hoffman [Fri, 9 Feb 2018 02:59:15 +0000 (21:59 -0500)]
Update documentation

21 months agoChange add.layers to support streaming sparse matrices
Paul Hoffman [Fri, 9 Feb 2018 02:58:54 +0000 (21:58 -0500)]
Change add.layers to support streaming sparse matrices

21 months agoFix documentation, add proper support for R sparse matrices
Paul Hoffman [Thu, 8 Feb 2018 15:34:29 +0000 (10:34 -0500)]
Fix documentation, add proper support for R sparse matrices

21 months agoremove extra comma, rerun docs
andrewwbutler [Wed, 7 Feb 2018 22:46:01 +0000 (17:46 -0500)]
remove extra comma, rerun docs

21 months agoChunk loomR::create
Paul Hoffman [Wed, 7 Feb 2018 22:38:51 +0000 (17:38 -0500)]
Chunk loomR::create

21 months agoMerge branch 'develop' of github.com:mojaveazure/loomR into develop
Paul Hoffman [Wed, 31 Jan 2018 00:03:36 +0000 (19:03 -0500)]
Merge branch 'develop' of github.com:mojaveazure/loomR into develop

21 months agoAdd support for multidimensional row- and column-attributes
Paul Hoffman [Wed, 31 Jan 2018 00:03:30 +0000 (19:03 -0500)]
Add support for multidimensional row- and column-attributes

21 months agoMerge pull request #4 from ChristophH/master
Paul Hoffman [Tue, 30 Jan 2018 22:51:33 +0000 (17:51 -0500)]
Merge pull request #4 from ChristophH/master

fix bug in create when checking chunk.dims length

21 months agoMerge pull request #5 from ChristophH/develop
Paul Hoffman [Tue, 30 Jan 2018 22:50:50 +0000 (17:50 -0500)]
Merge pull request #5 from ChristophH/develop

more flexible handling of result matrices when mapping functions

21 months agoallow more flexible results shapes when mapping a function
Christoph Hafemeister [Tue, 30 Jan 2018 22:40:03 +0000 (23:40 +0100)]
allow more flexible results shapes when mapping a function

21 months agoMerge branch 'master' into develop
Christoph Hafemeister [Tue, 30 Jan 2018 21:45:39 +0000 (22:45 +0100)]
Merge branch 'master' into develop

22 months agofix bug in create when checking chunk.dims length
ChristophH [Tue, 9 Jan 2018 12:43:09 +0000 (13:43 +0100)]
fix bug in create when checking chunk.dims length

22 months agoUse logging functions, change error messages, expand add.loom
Paul Hoffman [Wed, 3 Jan 2018 22:47:36 +0000 (17:47 -0500)]
Use logging functions, change error messages, expand add.loom

22 months agoAdd some new logging functions
Paul Hoffman [Wed, 3 Jan 2018 22:46:50 +0000 (17:46 -0500)]
Add some new logging functions

22 months agoFixes to add.cells, start add.loom
Paul Hoffman [Wed, 3 Jan 2018 19:54:13 +0000 (14:54 -0500)]
Fixes to add.cells, start add.loom

22 months agoMinor fix to subset.loom, added more to add.cells
Paul Hoffman [Tue, 2 Jan 2018 23:58:25 +0000 (18:58 -0500)]
Minor fix to subset.loom, added more to add.cells
Adding cells should work, haven't tested it yet so I can't say for sure

22 months agoAdd stuff for add.cells
Paul Hoffman [Tue, 19 Dec 2017 22:23:47 +0000 (14:23 -0800)]
Add stuff for add.cells

23 months agoFix display messages
Paul Hoffman [Wed, 13 Dec 2017 20:47:57 +0000 (15:47 -0500)]
Fix display messages

23 months agoMade changes and tested them, subset.loom works now (or in my one test it does)
Paul Hoffman [Wed, 13 Dec 2017 20:17:03 +0000 (15:17 -0500)]
Made changes and tested them, subset.loom works now (or in my one test it does)

23 months agoR doesn't evaluate variables in list creation...
Paul Hoffman [Wed, 13 Dec 2017 19:44:31 +0000 (14:44 -0500)]
R doesn't evaluate variables in list creation...

23 months agoI should fix create at some point...
Paul Hoffman [Wed, 13 Dec 2017 19:35:24 +0000 (14:35 -0500)]
I should fix create at some point...

23 months agoIf you're happy and you know it, syntax error!
Paul Hoffman [Wed, 13 Dec 2017 19:32:44 +0000 (14:32 -0500)]
If you're happy and you know it, syntax error!

23 months agoBecause I can't remember how my methods work...
Paul Hoffman [Wed, 13 Dec 2017 19:26:05 +0000 (14:26 -0500)]
Because I can't remember how my methods work...

23 months agoBug fix in create
Paul Hoffman [Wed, 13 Dec 2017 19:15:41 +0000 (14:15 -0500)]
Bug fix in create

23 months agoAdd some defaults to subset.loom
Paul Hoffman [Wed, 13 Dec 2017 19:06:23 +0000 (14:06 -0500)]
Add some defaults to subset.loom

23 months agoUpdate author list
Paul Hoffman [Wed, 13 Dec 2017 19:06:13 +0000 (14:06 -0500)]
Update author list

23 months agoUpdate description
Paul Hoffman [Wed, 13 Dec 2017 00:13:11 +0000 (19:13 -0500)]
Update description

23 months agoCleanup and reorganize code
Paul Hoffman [Wed, 13 Dec 2017 00:05:12 +0000 (19:05 -0500)]
Cleanup and reorganize code

23 months agoAdd subset function
Paul Hoffman [Tue, 12 Dec 2017 23:57:18 +0000 (18:57 -0500)]
Add subset function

23 months agoBegan support for selective-chunking in apply
Paul Hoffman [Tue, 12 Dec 2017 23:01:02 +0000 (18:01 -0500)]
Began support for selective-chunking in apply

23 months agoSlight refactoring
Paul Hoffman [Tue, 12 Dec 2017 18:58:26 +0000 (13:58 -0500)]
Slight refactoring

23 months agoadd ability to extract a dataframe of multiple row_attr or col_attr elements
Andrew Butler [Tue, 12 Dec 2017 15:29:26 +0000 (10:29 -0500)]
add ability to extract a dataframe of multiple row_attr or col_attr elements

2 years agoFixes to batch iteration. Allow skipping of validation due to issues with large datasets
Paul Hoffman [Thu, 16 Nov 2017 00:17:24 +0000 (19:17 -0500)]
Fixes to batch iteration. Allow skipping of validation due to issues with large datasets

2 years agoSyntax error
Paul Hoffman [Wed, 15 Nov 2017 21:21:09 +0000 (16:21 -0500)]
Syntax error

2 years agoBeginnings of add cells method
Paul Hoffman [Tue, 14 Nov 2017 22:56:41 +0000 (17:56 -0500)]
Beginnings of add cells method

2 years agoSyntax error
Paul Hoffman [Tue, 14 Nov 2017 20:00:35 +0000 (15:00 -0500)]
Syntax error

2 years agoMerge branch 'master' of github.com:mojaveazure/loomR
Paul Hoffman [Tue, 14 Nov 2017 19:19:54 +0000 (14:19 -0500)]
Merge branch 'master' of github.com:mojaveazure/loomR

2 years agoUse characters rather than 'versions' to store version information
Paul Hoffman [Tue, 14 Nov 2017 15:24:37 +0000 (10:24 -0500)]
Use characters rather than 'versions' to store version information

2 years agoAdd method to clean up object once garbage collected
Paul Hoffman [Thu, 9 Nov 2017 23:04:00 +0000 (18:04 -0500)]
Add method to clean up object once garbage collected

2 years agoUpdate README.md
Paul Hoffman [Thu, 9 Nov 2017 20:16:37 +0000 (15:16 -0500)]
Update README.md

2 years agoUpdate documentation
Paul Hoffman [Thu, 9 Nov 2017 19:29:28 +0000 (14:29 -0500)]
Update documentation

2 years agoFixed issues with chunking and iterating
Paul Hoffman [Thu, 9 Nov 2017 18:27:23 +0000 (13:27 -0500)]
Fixed issues with chunking and iterating

2 years agoUpdate issues with chunk iteration
Paul Hoffman [Thu, 9 Nov 2017 17:27:05 +0000 (12:27 -0500)]
Update issues with chunk iteration

2 years agoFix issue with adding attributes
Paul Hoffman [Thu, 9 Nov 2017 17:19:38 +0000 (12:19 -0500)]
Fix issue with adding attributes

2 years agoAdd overwrite to add layer and add atribute
Paul Hoffman [Thu, 9 Nov 2017 17:14:25 +0000 (12:14 -0500)]
Add overwrite to add layer and add atribute

2 years agochange margin to 1 for genes and 2 for cells
Paul Hoffman [Thu, 9 Nov 2017 16:31:24 +0000 (11:31 -0500)]
change margin to 1 for genes and 2 for cells

2 years agoupdate readme
Paul Hoffman [Wed, 8 Nov 2017 21:41:52 +0000 (16:41 -0500)]
update readme

2 years agoCleanup namespace
Paul Hoffman [Wed, 8 Nov 2017 13:54:52 +0000 (08:54 -0500)]
Cleanup namespace

2 years agoClean code
Paul Hoffman [Wed, 8 Nov 2017 00:58:07 +0000 (19:58 -0500)]
Clean code

2 years agoFixes and stuff
Paul Hoffman [Wed, 8 Nov 2017 00:56:09 +0000 (19:56 -0500)]
Fixes and stuff

2 years agoCheck for read-only mode, start add.cells/add.columns
Paul Hoffman [Tue, 7 Nov 2017 00:06:08 +0000 (19:06 -0500)]
Check for read-only mode, start add.cells/add.columns

2 years agoUpdate documentation
Paul Hoffman [Mon, 6 Nov 2017 19:40:55 +0000 (14:40 -0500)]
Update documentation

2 years agoGet apply working (I think), fix some stuff with map
Paul Hoffman [Mon, 6 Nov 2017 19:26:09 +0000 (14:26 -0500)]
Get apply working (I think), fix some stuff with map

2 years agoExpand apply, update documentation
Paul Hoffman [Fri, 3 Nov 2017 21:43:15 +0000 (17:43 -0400)]
Expand apply, update documentation

2 years agoFinished map and made it an R6 method
Paul Hoffman [Fri, 3 Nov 2017 20:30:54 +0000 (16:30 -0400)]
Finished map and made it an R6 method
Currently debating on whether or not to keep it as an S3 generic/method

2 years agoFIx issues where iterators and itertools weren't loading properly
Paul Hoffman [Fri, 3 Nov 2017 16:02:19 +0000 (12:02 -0400)]
FIx issues where iterators and itertools weren't loading properly

2 years agoFixed install issue while retaining S4
Paul Hoffman [Thu, 2 Nov 2017 21:06:50 +0000 (17:06 -0400)]
Fixed install issue while retaining S4

2 years agoRename file
Paul Hoffman [Thu, 2 Nov 2017 20:00:26 +0000 (16:00 -0400)]
Rename file

2 years agoAllow S4 methods to be set for loom
Paul Hoffman [Thu, 2 Nov 2017 19:58:17 +0000 (15:58 -0400)]
Allow S4 methods to be set for loom

2 years agoMap designed for R6(ish)
Paul Hoffman [Thu, 2 Nov 2017 19:57:47 +0000 (15:57 -0400)]
Map designed for R6(ish)

2 years agoUpdate README
Paul Hoffman [Wed, 1 Nov 2017 19:24:13 +0000 (15:24 -0400)]
Update README

2 years agoClean code, update documentation
Paul Hoffman [Wed, 1 Nov 2017 18:33:36 +0000 (14:33 -0400)]
Clean code, update documentation

2 years agoFix issues with create, further progress on batching
Paul Hoffman [Wed, 1 Nov 2017 17:22:17 +0000 (13:22 -0400)]
Fix issues with create, further progress on batching

2 years agoMerge branch 'master' of github.com:mojaveazure/loomR
Paul Hoffman [Tue, 31 Oct 2017 23:24:51 +0000 (19:24 -0400)]
Merge branch 'master' of github.com:mojaveazure/loomR

2 years agoBegun implementation of batch.scan
Paul Hoffman [Tue, 31 Oct 2017 23:24:32 +0000 (19:24 -0400)]
Begun implementation of batch.scan

2 years agofirst shell for CreateLoomFromSeurat
Rahul Satija [Tue, 31 Oct 2017 23:02:30 +0000 (19:02 -0400)]
first shell for CreateLoomFromSeurat

2 years agoFinish layer adding
Paul Hoffman [Tue, 31 Oct 2017 22:24:26 +0000 (18:24 -0400)]
Finish layer adding

2 years agoUpdate how layers are added to a loom object
Paul Hoffman [Tue, 31 Oct 2017 22:22:19 +0000 (18:22 -0400)]
Update how layers are added to a loom object

2 years agoFix issue where the H5D for '/matrix' wasn't being stored
Paul Hoffman [Tue, 31 Oct 2017 19:57:43 +0000 (15:57 -0400)]
Fix issue where the H5D for '/matrix' wasn't being stored