137 Commits

Author SHA1 Message Date
Bruce Martin
0aa0f641ab improve selection interaction with clip changes (#744)
* brush interactions with underlying dataframe updates improved

* improve comment

* reset selection state upon clip
2019-05-03 11:14:30 -07:00
Colin Megill
86bf64e793 avoid overflow on clip dialogue (#740) 2019-05-01 15:41:54 -04:00
Sidney Bell
a08e19bbd0 Clip continuous values based on percentile cutoffs (#672)
* Add numeric inputs for percentiles

* Define initial values for percentile cutoffs in world reducer

* add percentil to crossfilter dimensions

* worldEqUniverse now handles cloned worlds

* add Dataframe.mapColumns

* Wire up handlers for percentile inputs

* World reducer and stateManager know about continuousPercentileMin/Max

* Create world as universe clone (not pointer) to avoid clobbering vals

* Define basic actions for setting continuousPercentileMin/Max

* Under the hood, deal with percentiles between 0 and 1

* Move percentile inputs to visualization settings menu

* Fix padding for undo/redo buttons

* Trigger world rebuild from percentile actions

* BROKEN - pseudocode for clamping dataframe by percentiles upon world rebuild

* fix error handling on clip quantiles; start world clipping implementation

* more unclipped reorg

* rename crossfilter.percentile to quantile

* simplify schema access

* update continuous legend when scale changes

* update color cache when clip changes

* clip obs annotations and var data when clip quantile changes

* use own fromEntries

* fix tests

* stable non-finite float sort/search

* clarify comments

* fix syntax typo

* use new stand-alone clip

* clip expresssion data

* add select tests for non-finite scalars

* basic styles

* clip UI now requires explicit commit

* reset enable/disable accounts for clip percentiles

* better error messages

* fix bug in undo interaction with programatic min brush selection

* small refactoring

* support clipping of int data

* do not perform unnecessary summarizations

* improve caching of dataframe compiled columns

* add percentile precompute to Dataframe.summarize

* use Dataframe.summarize for clip percentiles

* remove obsolete quantile code from corssfilter

* histogram scale and label Y axis, add unclipped X range labels

* layout tweaks

* scatterplot now updates when clip changes

* improve comments

* remove debugging comment

* rework clip number entry validation for usability

* ui tweaks to histogram colors and layout

* enable undo/redo for clip user action

* refine UI on clip value entry

* api cleanup

* update confusing comment

* clarify purpose of isValidDigitKeyEvent

* fix misleading comment

* apply appropriate button-group classes; do not mix span and div

* variable name and comment changes suggested in PR review

* rename sort to sortArray; remove unused and dead code path

* naming changes suggested in PR review

* code review improvements for clarity

* more small changes from PR review

* lint fixes for PR review

* fix spelling error

* clarify that function performs in-place modification of world

* add comment to clarify intent of range operation

* fix bad indents in comments

* clean up __columnsAccessor comments and code

* improve comments around clipPredicate

* field name consistency

* improve comment on quantiles params
2019-04-30 16:20:10 -07:00
Justin Kiggins
1f735abe2b updates the roadmap & reorganizes the README (#712) 2019-04-18 13:10:03 -07:00
Colin Megill
b878b0f93c Gene typeahead stale state (#714)
* reimplementing suggest

* resolve stale state
2019-04-17 14:03:10 -04:00
Bruce Martin
9044b8d85d fix color-by regression in toggle (#705)
* fix color-by regression in toggle

* fix incorrect field reference
2019-04-11 12:47:38 -07:00
Bruce Martin
5e02408732 latent bug in color toggle (#701) 2019-04-09 10:50:35 -07:00
Bruce Martin
7275d9d4dc Graph selection state management and history bug fixes (#679)
* save graph selection in redux state

* fix old graph brush select regressions

* refactor graph brush selection to work with undo/redo

* update tests to match new crossfilter spatial select API

* graph selection state now in redux

* remove dead code

* sync graph selection with redux state; improvements to undoable machinery

* fix regression in undoable

* differentiate graph selection cancel from deselect action

* simplify calculation

* remove debugging code

* fix responsive repaint bug in graph selection tool

* undoable debugging and code cleanliness

* undoable action filter state now merges, rather than replaces

* improve comments

* add debounce to undoable action filter; improve comments and debug sanity check code

* comments

* fix undoable bug with clear scatterplot actions

* disable undoable debug flag

* cleanup API and comments around statemachine

* add test id attribute to lasso

* add better error handling for gene fetch requests
2019-04-08 15:53:12 -07:00
Charlotte Weaver
c9a8e3ea42 Add manual UX tests (#699) 2019-04-08 13:23:17 -07:00
Bruce Martin
71505abe4c toggle color-by when repeatedly picked by the user (#696)
* toggle color-by when repeatedly picked

* remove debugging code
2019-04-08 10:57:47 -07:00
Charlotte Weaver
5d4b11d287 Better smoke tests (#669) 2019-03-28 16:47:42 -07:00
Charlotte Weaver
096d477893 use Math.abs when calculating lasso area (#673) 2019-03-27 21:02:31 -07:00
Bruce Martin
153f240c43 brushable histogram brush selection responds to state updates (#670)
* add continuousSelection reducer and make histo respond to state changes

* correctly handle uninitialized state for brush move

* PR review tweaks
2019-03-25 15:02:39 -07:00
Bruce Martin
7ef5203564 Undo/redo (#659)
* immutable crossfilter

* first cut at reducer refactor with cascade model

* add initial redo/undo implementation

* small optimization

* integrate expression with history

* add tests for new reducers and fix a couple of small initialization bugs

* treat tiny lasso selections as a clear

* better function name for clarity

* fix undo for differential expression

* remove logging

* fix regression due to bad merge

* cleanup and comments for clarity

* improve undoable configuration for flexibility

* fix stale comments

* remove debugging code from production build

* rename categoricalSelectionState

* rename file

* improve comments
2019-03-22 14:53:48 -07:00
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
571b7387e7 remove dead code from globals (#651) 2019-03-19 06:22:39 -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
Bruce Martin
495dc55144 remove obsolete URL middleware (#639) 2019-03-11 16:03:33 -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
a876740a3c create helper file for controls reducer (#615)
* 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

* create helper file for controls reducer
2019-02-28 09:21:19 -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
Charlotte Weaver
585a5808b9 check if accept type in content type string (#589) 2019-02-08 09:41:24 -08:00
Bruce Martin
6f464f4f92 package dependency updates (#585)
* lint

* update dev-related package dependencies
2019-02-06 12:57:09 -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
3bfeadc2b9 improve handling of non-finite floating point values (#490)
* improve HTTP error reporting

* generate standards-compatible JSON

* add --nan-to-num work-around for non-finite floating point values

* lint

* update tests

* correctly set Infinities to min/max

* REAMDE update for --nan-to-num

* define constant for repetitive warning message

* clarify where NaN errors will occure
2018-12-04 14:56:16 -08:00
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