Commit Graph

91 Commits

Author SHA1 Message Date
Colin Megill
016a4a422a Procedurally resize brush (#650)
* add on brush end event

* brush snap move

* resize brush
2019-03-20 14:46:20 -07:00
Bruce Martin
996b06cecc refactoring - immutable crossfilter (#647)
* immutable crossfilter

* PR review changes
2019-03-20 14:32:35 -07:00
Bruce Martin
aa5ce4a2f1 correctly toggle group selection in categorical metadata (#640) 2019-03-12 10:49:29 -07:00
Bruce Martin
80969012c9 do not reset color scale when dismissing scatterplot (#637) 2019-03-12 10:49:01 -07:00
Bruce Martin
caaee7e9bf do not reset color-by when subsetting world (#636)
* do not reset colors when subsetting to world

* revert diffexp state change
2019-03-12 10:48:35 -07:00
Colin Megill
8795f0f32c Add test ids and classes (#633)
* data test ids and classes

* suggest
2019-03-07 13:01:41 -08:00
Colin Megill
a0f54b4871 Add menu (#631)
* add menu

* Added library versions to config

and tests

* add template version number
2019-03-06 11:56:46 -05:00
Bruce Martin
3d6df0c044 implement improved disable/enable of Reset UI (#628) 2019-03-05 08:38:55 -08:00
Bruce Martin
e7ad6f5d1c [WIP DO NOT MERGE] correctly display graph legend for negative continuous metadata (#620)
correctly display graph legend for negative continuous metadata
2019-02-28 09:08:19 -08:00
Bruce Martin
2f1facaafb [WIP DO NOT MERGE] suppress display of continous annotation without a finite extent (#618)
* initial dataframe commit

* initial dataframe port of core app

* rename variables for clarity

* remove unused import

* comment out unused code

* fix array handling bug in crossfilter dimension creation

* allow creation of empty dataframes

* handle non-existent columns

* handle non-existent columns

* revise tests for new dataframe

* comments for clarity

* comments for clarity

* generate bulk add placeholder with real gene names

* fix bug in gene name adding

* more dataframe unit tests

* fix bug - subset from current world, not universe

* put cut and pasted code into a single function

* improve caching of crossfilter

* remove cascading update bug from graph

* more performance work

* improve state handling for scatterplot

* performance optimization of critical path

* add column summarization

* dataframe utils

* add callOnceLazy

* fix tests

* minor updates found during review

* fix misspelling

* remove RESTv02 from function names

* comment cleanup

* cut/icut col parameter defaults to null

* break up large test

* improve tests and comments on dataframe at/has functions

* add Dataframe withCol/dropCol

* expression varData now stored in a dataframe

* dead code cleanup

* use dataframe.summarize()

* test cases for Dataframe.col.summarize

* update test cases for new dataframe summarize

* improve naming

* use new hasCol API

* add comments

* add more Dataframe.withCol tests

* add ability to specify row index in cut operation

* retire subsetVarData function

* correctly handle expression subsetting

* lint and improve comments

* rename cut to subset

* suppress display of continous annotation withont a finite extent

* fix botched merge

* more fix of botched merged
2019-02-28 09:05:48 -08:00
Bruce Martin
ffd6273419 Dataframe, part deux - add varData and summarize() (#608)
* initial dataframe commit

* initial dataframe port of core app

* rename variables for clarity

* remove unused import

* comment out unused code

* fix array handling bug in crossfilter dimension creation

* allow creation of empty dataframes

* handle non-existent columns

* handle non-existent columns

* revise tests for new dataframe

* comments for clarity

* comments for clarity

* generate bulk add placeholder with real gene names

* fix bug in gene name adding

* more dataframe unit tests

* fix bug - subset from current world, not universe

* put cut and pasted code into a single function

* improve caching of crossfilter

* remove cascading update bug from graph

* more performance work

* improve state handling for scatterplot

* performance optimization of critical path

* add column summarization

* dataframe utils

* add callOnceLazy

* fix tests

* minor updates found during review

* fix misspelling

* remove RESTv02 from function names

* comment cleanup

* cut/icut col parameter defaults to null

* break up large test

* improve tests and comments on dataframe at/has functions

* add Dataframe withCol/dropCol

* expression varData now stored in a dataframe

* dead code cleanup

* use dataframe.summarize()

* test cases for Dataframe.col.summarize

* update test cases for new dataframe summarize

* improve naming

* use new hasCol API

* add comments

* add more Dataframe.withCol tests

* add ability to specify row index in cut operation

* retire subsetVarData function

* correctly handle expression subsetting

* lint and improve comments

* rename cut to subset

* changes based on PR review
2019-02-28 08:34:22 -08:00
Charlotte Weaver
2bae696986 Smoke tests (#604)
smoke tests
2019-02-27 15:46:58 -08:00
Bruce Martin
6b33315cbe Dataframe (#576)
* initial dataframe commit

* initial dataframe port of core app

* rename variables for clarity

* remove unused import

* comment out unused code

* fix array handling bug in crossfilter dimension creation

* allow creation of empty dataframes

* handle non-existent columns

* handle non-existent columns

* revise tests for new dataframe

* comments for clarity

* comments for clarity

* generate bulk add placeholder with real gene names

* fix bug in gene name adding

* more dataframe unit tests

* fix bug - subset from current world, not universe

* put cut and pasted code into a single function

* improve caching of crossfilter

* remove cascading update bug from graph

* more performance work

* improve state handling for scatterplot

* performance optimization of critical path

* add column summarization

* dataframe utils

* add callOnceLazy

* fix tests

* minor updates found during review

* fix misspelling

* remove RESTv02 from function names

* comment cleanup

* cut/icut col parameter defaults to null

* break up large test

* improve tests and comments on dataframe at/has functions
2019-02-22 11:31:34 -08:00
Colin Megill
dbb3a309a9 Lasso (#586)
* lasso working

* break out invert into own function

* action

* add spatial dimension to crossfilter, in support of polygon lasso

* improve comments on new dimension API

* lasso vs zoom
2019-02-08 11:48:51 -08:00
Colin Megill
08ea7d5137 Better input validation (#580) 2019-02-05 10:44:59 -05:00
Colin Megill
2df7161cd8 Bulk add genes (#567)
* bulk add

* cleanup
2019-01-29 16:26:09 -05:00
Colin Megill
3fa888c6d4 user defined gene sets scatterplot, remove works (#556) 2019-01-16 03:37:08 -05:00
Colin Megill
a42c9aca1c resetting interface spinner but locked interface (#555) 2019-01-16 03:36:35 -05:00
Bruce Martin
b90447c387 binary wire format with flatbuffers (#509)
* first flatbuffer schema

* do not lint auto-generated files

* add flatbuffers package

* add flatbuffer module

* wire up /data/X/T route

* use flatbuffers for matrix data fetc

* clarity and comments

* add flatbuffer layout route

* clean up obsolete code

* fix tests

* move flake8 config to setup.cfg

* add comments

* lint

* rework layout routes for fbs

* add more type support to fbs

* lint

* add flatbuffer support for annotations

* function name improvements

* fix botched merge with master

* remove unused import

* route cleanup for flatbuffers

* rename function for clarity

* add missing globals to Jest tests

* fix client JS tests

* fix routes for Python tests

* comments for clarity

* non-finite floating point hardening

* more non-finite number handling

* lint

* fix tests for summarizeAnnotations

* harden diffexp calculation against FP errors

* cleanup unused code

* lint

* add encoding tests for flatbuffers

* application type specified as strings

* fix spelling error

* improve variable names

* add note about documentation gap

* rename FBS DataFrame to Matrix
2019-01-09 14:26:05 -08:00
Colin Megill
42e25a1a1f Async on long running operations (#543)
* compute differential button

* add user gene loading state to reducer

* create input group, consume usergeneloading

* add loading state
2019-01-07 16:45:47 -05:00
Colin Megill
b0daeb3a9b disable cell set buttons (#538) 2019-01-03 20:05:09 -05:00
Bruce Martin
cfcf16aa69 [DO NOT MERGE] performance improvements in color-by feature (#535)
performance improvements in color-by feature
2018-12-27 14:05:49 -08:00
Colin Megill
0ef6c36f4c Cluster Occupancy (n dim cube) (#513)
* create occupancy component

* occupancy working

* centering, width, flex spacing

* add is-number

* extend sort to cover string + int

* proof of concept sorted occupancy

* handle undefined occupancy entry, cleanup

* only render occupancy when colorby is cat

* cleanup unused vars

* cleanup
2018-12-17 14:19:48 -05:00
Bruce Martin
296ed752fa Improved summary counts of annotation values (#478)
* convert annotation summary to a Map

* add 2d annotation count summary

* add memoization on 2D annotation counting

* add tests for annotation summarization

* fix import/exports

* rename WorldOps to WorldUtil

* rename WorldOps to WorldUtil

* add comment
2018-12-03 09:15:03 -08:00
Bruce Martin
af0d1f6fb2 issue #480 workaround (#484)
* only load annotation var names

* remove incorrect usage of var annotation data

* temporary workaround for issue #480

* lint

* issue warnings only once per item
2018-11-29 16:33:21 -08:00
Colin Megill
00b9a8fa72 Fuzzy search on genes (#473)
* proof of concept blueprint typeahead

* poc with fuzzysearch lib

* typeahead adds gene on enter

* add gene on menu click

* typeahead clears correctly

* cleanup
2018-11-28 09:50:02 -08:00
Bruce Martin
933fac5fff Allow float64 to down-cast to float32 (#472)
* warn if annotations will down-cast to float32

* correctly handle falsey data values
2018-11-27 11:17:30 -08:00
Bruce Martin
138d30909a improve type handling for non-string annotation data (#465)
* improve type handling for non-string annotation data

* improve clarity of code
2018-11-26 10:32:29 -08:00
Jeremy Freeman
dff2526077 warm to cool (#454) 2018-11-16 14:33:32 -08:00
Colin Megill
ef80c8df2a Change color scales to rainbow (#449)
* rainbow

* eslint

* remove comments
2018-11-15 18:17:55 -08:00
Bruce Martin
00a68276a2 diffexp performance & UX improvements (#431)
* new diffexp REST API spec

* new diffexp REST API; faster diffexp and dataframe slicing

* first draft of fast diffexp

* convert variance calculation to two-pass method

* lint

* update front-end use of API

* fix typo in spec

* disable content compression

* catch index filter format errors

* clean up of dead code

* resolve PR review comments
2018-11-14 12:51:24 -08:00
Colin Megill
dbff824854 Viewport fills entire screen (#430)
* full pane webgl and svg

* fixes for full pane selection and centering

* force graph remount, clear brush state
2018-11-13 11:45:38 -05:00
Colin Megill
9decf134e0 fixed scatterplot infinite render (#429)
* add more to state from componentDidMount

* always brush

* destructure

* move render to function

* fixed scatterplot infinite render

* remove logging
2018-11-09 20:28:22 -05:00
Colin Megill
0dcc17d6d5 rerender axes on regraph (#403)
* remove cells loading now that we have toast

* rerender histogram axes

* remove logging
2018-11-05 09:29:49 -05:00
Bruce Martin
9d7754e31e Improve front-end HTTP error handling (#397)
* UI for HTTP error handing in diffexp route

* HTTP error handling for other routes

* clean up toasters
2018-10-30 19:02:11 -07:00
Bruce Martin
bc15e9229f update config params to match REST API spec (#393) 2018-10-30 11:03:40 -07:00
Colin Megill
ed66ae6e4a tooltips, copy, scatterplot tray (#383)
* tooltips, copy, scatterplot tray

* reset interface

* copy
2018-10-26 19:21:39 -04:00
Colin Megill
d221d76be6 test for world, graph border, legend label (#378)
* test for world, graph border, legend label

* typo
2018-10-25 12:16:55 -04:00
Colin Megill
7aa390b5a1 left sidebar improvements (#368)
* left sidebar improvements

* lint
2018-10-24 10:21:18 -04:00
Colin Megill
96675f806c hotfix duplicate globals declaration 2018-10-22 16:39:41 -04:00
Colin Megill
df671192be Begin integrating blueprint (#359)
* toast test

* modify webpack build to allow for global CSS; use CSS modules to scope component styling

* remove heatmap

* add label to index resets

* swapping out buttons for blueprint

* adding constants to globals

* swapping out blueprint buttons

* title position, sidebar improvements

* sidebar styles

* adding toasts for validation errors

* zebra section trial

* integrating blueprint, switching buttons over, breaking out scatter

* clean up console
2018-10-22 15:46:37 -04:00
Bruce Martin
0c271bc815 categorical metadata performance work (#356)
* do not create unecessary option state for categories we will not display

* performance improvements for categorical metadata handling
2018-10-22 09:56:41 -07:00
Bruce Martin
5dea303bcd handle case of excessively large number of options in categorical met… (#350)
* handle case of excessively large number of options in categorical metadata
* move max category options count into globals
2018-10-18 18:07:39 -07:00
Bruce Martin
f9f43c42c0 more lint - components (#336)
* more lint

* fix typo introduced in delinting

* more lint

* remove dead code

* lint fixes

* lint
2018-10-17 07:17:51 -07:00
Colin Megill
952578680a Remove heatmap, add diffexp info to histograms (#339)
* Create Release_Validation_Recipe.md

* compose middle ware for redux devtools

* update package.json and lock

* remove heatmap, add to left side bar

* redux devtools extension
2018-10-16 16:29:20 -07:00
Bruce Martin
6b0aafd27c package dependency cleanup (#330)
* update npm packages.  babel 7, redux 4, etc

* remove obsolete babel config file

* use correct icons
2018-10-15 17:36:13 -07:00
Colin Megill
8e08534d42 user defined gene 2018-10-15 11:20:52 -07:00
Colin Megill
2b77f8146b namespacing 2018-10-15 11:20:52 -07:00
Colin Megill
48fa221ad9 diffexp, regraph, brush 2018-10-15 11:20:52 -07:00
Colin Megill
fff331e1f0 stub additional validation for gene name 2018-10-15 11:20:52 -07:00