Severiano Badajoz
c983e878e9
fix incorrect gene add error on empty query ( #910 )
...
* fix add gene button
* make bulk add case insensitive
* increase performance, incl memoizing
* change which lists are memoized
* improve hash to use ID from dataframe column
* Add requested fixes, and actually make bulk add work
* add default result to empty gene query
* replace with unicode ellipses
* change empty message
2019-09-23 16:31:07 -07:00
Severiano Badajoz
077541c762
fix bugs surrounding gene adding ( #919 )
...
* fix add gene button
* make bulk add case insensitive
* increase performance, incl memoizing
* change which lists are memoized
* improve hash to use ID from dataframe column
* Add requested fixes, and actually make bulk add work
2019-09-23 16:30:53 -07:00
Bruce Martin
3d15db7c5e
parameterize pbmc3k scanpy engine test ( #939 )
2019-09-20 17:41:32 -07:00
Bruce Martin
109c9e70ec
Add obs index to label file ( #928 )
...
* remove debug logging
* load and save obs/row index in label file
* lint
* update tests
2019-09-19 09:16:01 -07:00
Colin Megill
197ea9214a
fix italic ( #935 )
2019-09-18 19:36:49 -04:00
Colin Megill
81e57afe29
Anno fixes (easy) ( #925 )
...
* change wording from value to label
* tooltip position
* Padding for text & code whitespace
2019-09-18 19:22:51 -04:00
Bruce Martin
3660a6cc27
Experimental - manual annotations ( #837 )
...
* icons, partway
* redux for values
* onChange
* cancel
* annotations lifecycle for category names
* copy categorical
* edit category
* add Dataframe.withColsFrom
* render user annotations; default add/delete annotation category
* add label name to actions
* category name edit
* error checking improvements
* change schema field isUserAnnotation to writable
* always have an unassigned label; implement delete label
* implement add new label and edit label name
* label current cell selection
* fix select exact bug in crossfilter
* clean up categorical reducer
* fix tests
* remove debugging printf
* implement subset/reset for user annotations
* undo redo support for user annotations
* remove duplicate button from categories
* add modal
* remove obsolete duplicate annotation reducers
* remove old debugging printf
* connect modal to annotation create and dup
* initial full-stack wiring
* finish up end-to-end wiring
* fix existing unit tests
* fix pytests to match new schema API
* remove debugging printfs
* add label file rotation
* remove obsolete comment
* add fbs encode/decode tests
* add tests for writable annotations
* simplify code
* fix hashing bug with FBS encoding
* lint
* fix smoke tests
* improve error checking in Dataframe.withColsFrom
* add unit test for Dataframe.withColsFrom
* add unit test for Dataframe.columns and Dataframe.renameCol
* fix bug in FBS encode, add better error checks, refactor
* add FBS encode/decode test
* add clarifying comment
* clean up action type names; fix state inconsistency in crossfilter update
* change autosave timer to 2.5sec
* sort categorical metadata render order so it remains consistent
* add temporary autogenerated label for add-new-label operation
* fix hover-over label menu interference with cell highlighting
* remove debugging code
* add missing reducer cases & fix typo
* make dataframe memoize more general purpose
* add dev mode for annos
* fix error on select duplicate
* handle zero occupancy categories
* correctly maintain unclipped AND clipped world
* correctly handle zero length FBS matrix and label files
* ensure all writable categorical schema contains an unassigned category
* handle case where building occupancy stack for category with no members
* dialog for creating label, disable button if duplicate or empty
* visually separate writeable
* edit category
* fix edit category name
* remove debugging code
* fix edit annotation label
* visually define unassigned, change options
* Pull in requirements.txt from `master`
* label currently selected cells
* duplicate label
* lint
* fix pytest merge issues
* rename --label-file to --experimental-label-file
* remove debugging console log
* spelling error fix; fix bug found in PR review.
* lint
2019-09-18 07:33:41 -04:00
Bruce Martin
ab2c423006
JS package updates ( #922 )
2019-09-17 09:36:47 -07:00
Bruce Martin
922c375333
Rename "layout" to "embedding" in the UI ( #921 )
...
* rename "layout" to "embedding" in the UI
* docs changes for layout
* fix typo in data docs
* new help text, per PR review
2019-09-16 15:34:14 -07:00
Colin Megill
ec4da63408
Format histogram axes: 200,000 --> 200k ( #913 )
...
* remove dead file
* tickformat
2019-09-16 17:07:51 -04:00
Bruce Martin
20317fd08f
Add URL data locators to launch sub-command ( #920 )
...
* initial commit of URL support for launch
* lint
* modify tests to use new data locator
* add locator unit tests
* fix typo in faq
* more lint
* update faq per PR review
2019-09-15 09:01:53 -07:00
Charlotte Weaver
0f520f2fd4
[Merge on next release] Document how to install cellxgene prepare ( #889 )
...
* Document how to install cellxgene prepare
after pr #887 merged
* formatting
* remove reference to cellxgene[louvain]
2019-09-13 18:15:06 -07:00
Bruce Martin
84c815cc04
pin h5py to 2.9.0 to temporarily work around regression ( #916 )
2019-09-11 13:20:15 -07:00
Charlotte Weaver
77de22d1ed
merge louvain and prepare extra requires ( #897 )
2019-08-29 12:49:19 -07:00
Bruce Martin
c35f94fe6d
add constraints on pan and zoom-over point ( #904 )
2019-08-28 17:56:46 -07:00
Bruce Martin
78a43402cb
package dep update ( #905 )
2019-08-28 09:11:10 -07:00
Bruce Martin
b0562a11fd
scale point size for graph and scatter plots ( #903 )
...
* scale point size for graph and scatter plots
* improve comments
2019-08-27 14:12:53 -07:00
Bruce Martin
b309367bb0
Add hover-over highlighting to the scatterplot ( #900 )
...
* small perf improvement - do not recreate functions each time component is updated
* add hover-over highlighting to scatterplot
2019-08-27 14:01:30 -07:00
Bruce Martin
b359a610da
tooltips improvements ( #896 )
...
* add and fix tooltips on toolbar
* move tooltips below buttons
* add global definition for tooltip hover over delay
2019-08-22 20:56:33 -07:00
Bruce Martin
0f36b49840
Graph/scatterplot improvements ( #893 )
...
* many graph/scatterplot fixes: 722, 882, 758, 886
* fix e2e test breakage caused by graph transform work
* convert webgl point shaders to use flags rather than explicit point size
* remove unused packages from dependencies
* fix typo in regl prop name
* factor common code into util helper file
* legibility tweaks
2019-08-22 20:56:05 -07:00
Charlotte Weaver
28c4d28308
extract prepare from main install ( #887 )
...
* extract prepare from main install
* add requirements-prepare to manifest
2019-08-21 14:26:01 -07:00
Charlotte Weaver
b8c05763fe
sparse tests ( #894 )
2019-08-21 14:09:36 -07:00
Charlotte Weaver
613f1a911f
pin matplotlib dependency ( #885 )
...
reordering packages does not work from dist install
2019-08-14 14:21:07 -07:00
bbb521537b
create single-click Heroku hosting and documenation ( #834 )
...
* add deploy button
* Fix info
* Create heroku.yml
* Remove unnecessary files
* add buildpack
* Add container stack
* Remove comment
* Remove comment
* fix stack name?
* Move run to heroku.yml with port var
* Add dataset env var
* Add dataset env var
* Revert "Remove unnecessary files"
This reverts commit b2cb34dccbcharlottesweaver@gmail.com >
* fix link
Co-Authored-By: Charlotte Weaver <charlottesweaver@gmail.com >
* replace github links with S3 buckets
* small fixes
* grammar and spelling changes
* add hibernation caveat
* more spelling
* revise what is heroku
* rewording
* rename header
* revise caveats
* Update experiments/heroku/README.md
Co-Authored-By: Charlotte Weaver <charlottesweaver@gmail.com >
* Update experiments/heroku/README.md
Co-Authored-By: Charlotte Weaver <charlottesweaver@gmail.com >
* Update experiments/heroku/README.md
Co-Authored-By: Charlotte Weaver <charlottesweaver@gmail.com >
* Update experiments/heroku/README.md
Co-Authored-By: Charlotte Weaver <charlottesweaver@gmail.com >
* Update experiments/heroku/README.md
Co-Authored-By: Charlotte Weaver <charlottesweaver@gmail.com >
* Update experiments/heroku/README.md
Co-Authored-By: Charlotte Weaver <charlottesweaver@gmail.com >
* various changes
* Update experiments/heroku/README.md
Co-Authored-By: Charlotte Weaver <charlottesweaver@gmail.com >
* Update experiments/heroku/README.md
Co-Authored-By: Charlotte Weaver <charlottesweaver@gmail.com >
* Update experiments/heroku/README.md
Co-Authored-By: Charlotte Weaver <charlottesweaver@gmail.com >
* Update experiments/heroku/README.md
Co-Authored-By: Charlotte Weaver <charlottesweaver@gmail.com >
* Update experiments/heroku/README.md
Co-Authored-By: Sidney Bell <sidneymbell@users.noreply.github.com >
* Update experiments/heroku/README.md
Co-Authored-By: Sidney Bell <sidneymbell@users.noreply.github.com >
* revisions/additions
2019-08-14 13:16:49 -07:00
Charlotte Weaver
79a503e436
fix bad matplotlib library by installing scanpy first ( #881 )
2019-08-12 16:42:26 -07:00
Sidney Bell
69e69f4dae
Add logo and favicon to docs ( #880 )
2019-08-12 16:03:41 -07:00
Sidney Bell
fcaa30d7cc
readme updates ( #878 )
...
* Add Lia to core team in readme
* Update readme
* Add logo to readme
2019-08-12 12:56:26 -07:00
Colin Megill
03baa1ac0b
overflow title ( #858 )
2019-08-05 14:08:41 -04:00
Bruce Martin
906d65c06f
fix binning error in continuous data histogram ( #869 )
2019-08-05 10:40:56 -07:00
Justin Kiggins
57b1c3cbb4
put badges on one line in README ( #862 )
2019-07-31 16:01:09 -07:00
Marcio von Muhlen
40c533a45b
Update README.md ( #856 )
...
Full URLs for roadmap, contributor guide to fix 404s on Pypy.
2019-07-26 13:35:46 -07:00
Severiano Badajoz and Justin Kiggins
9eb8185e82
add badges to readme ( #857 )
...
* prettier
* add pypi and commit badges
* formatting
* revert DOI badge
* Update README.md
Co-Authored-By: Justin Kiggins <justin.kiggins@chanzuckerberg.com >
2019-07-25 16:52:38 -07:00
Charlotte Weaver
6a86883c2d
Remove stray quote ( #854 )
2019-07-19 12:40:54 -07:00
Colin Megill
d16a69e158
bump version to 0.11.0 ( #850 )
...
* bump version to 0.11.0
* manually fix version number
2019-07-16 14:27:41 -04:00
Severiano Badajoz
3d6bb88556
improve performance around category highlighting ( #849 )
...
* remove function call and add comment
* separate crossfilter size calc into memoized function
2019-07-15 16:00:23 -07:00
Bruce Martin
e199b14259
correctly handle float columns which only contain NaN ( #848 )
2019-07-15 14:49:33 -07:00
Severiano Badajoz
9c05aa6766
remove selection interaction from categorical value label ( #847 )
2019-07-15 11:32:42 -07:00
Severiano Badajoz
3833bada54
style mini-histogram popups ( #845 )
...
* popup styling changes
* change to target hover only and change delay
* change popover wording
* change popover wording
2019-07-13 16:52:00 -07:00
Charlotte Weaver
3d98797d8c
Installer ( #840 )
2019-07-12 12:29:22 -07:00
Colin Megill
777214cc14
upgrade lodash ( #844 )
2019-07-11 18:35:57 -04:00
Severiano Badajoz
9f0f60b5eb
add point dilatation on hover ( #841 )
...
* enable centroid
* introduce new sizing
* scale point size based off hovered category
* add styling
* fix margins
* disable centroid labels
* remove unused code and add detail to comment
* remove cell dilation on selection toggle
* move hover to name label
* hover on value except for checkbox
* add border radius to value
2019-07-11 15:33:44 -07:00
Severiano Badajoz
ca20add577
reset colorAccessor and colorMode if colored diffexp gene is removed ( #843 )
...
* add action to clear colorMode and colorAccessor if diffexp is removed
* create new colorHelper function
* creater colorHelper for conditionally setting state
* add abbr
* revert abbr
2019-07-11 14:12:38 -07:00
Sidney Bell
98b07b1284
Add code of conduct; move contributing guidelines to CONTRIBUTING.md ( #842 )
2019-07-11 10:09:35 -07:00
Severiano Badajoz
941c297363
categorical vs continuous mini histograms ( #827 )
...
* comment
* add histogram functionality to Dataframe; port category occupancy to use it
* fix binning and create histogram for continous by catagorical
* Remove unnecessary logs
* Begin work on KDE
* Replace broken KDE with working histogram
* Define domain and range based on data from histogram
* Fix occupancy
* Add continuous obs and switch to canvas
* Stop value from always rerendering
* clear before render
* Clear canvas on render
* refactor categorical occupancy to canvas
* Remove log
* simplify finding max
* refactor kde->histogram and occupancy->bins
* refactor svg -> canvas
* rename to occupancy stack
* create popup
* add metadata and categorical values to popup
* fix overflow
* remove zeros info
* style graph
* fix shouldComponentUpdate to look for world changes
* change categorySelected -> categoryValueSelected
* refactor out render
* remove comment
* conditionally have bottom border
* remove diff comp
* remove comments
* remove unnecessary mapping
* Add comments describing drawing functions
* comments
* flip comparison order
* remove logging
* move default to parameter
* move defaults to parameter
* disable popover if not showing histogram
* fix wording and styling
* add line break
2019-07-09 11:19:01 -07:00
Charlotte Weaver
722a91f1d2
remove options widget + launch on file selection ( #839 )
...
* remove options widget + launch on file selection
* extend drop area width
2019-07-09 10:46:13 -07:00
Severiano Badajoz
acdc810f82
disable centroids ( #833 )
...
* disable hover actions
* Remove action firing
* Remove disabled on action type and leave function call commented
2019-07-08 15:15:50 -07:00
Charlotte Weaver
8afb22a017
GUI UI Elements ( #816 )
2019-06-27 17:30:57 -07:00
Charlotte Weaver
5effe4bbbb
removed --diffexp cli param ( #826 )
2019-06-26 14:46:58 -07:00
Justin Kiggins
df1109e920
updating roadmap ( #825 )
2019-06-26 09:47:37 -07:00
Sidney Bell
2df93d6d94
Add prepare example and update demo datasets ( #810 )
...
* Update example datasets w/ pbmc3k and tabula muris
* Add `prepare` overview and example
* Add S3 data links
* Incorporate PR feedback & copyedits
* Switch to letter pointers
* unix line endings
* path
2019-06-13 16:55:09 -07:00
Severiano Badajoz