Commit Graph
245 Commits
Author SHA1 Message Date
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 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 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
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
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
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
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
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
Severiano Badajoz 334b8bb8da draw labels marking the centroids of category value clusters (#809)
* Connect mouse over events to reducer actions

* Change Styling on hover

* Rename reducer actions to be more descriptive

* Reorder reducer in cascade

* Create centroid calculation util

* Whitespace

* Typo fix, use correct action

* Create centroid calc util

* Create centroid svg setup

* Refactor existing svg layer to toolSVG

* Change calcCentroid signature and centroidXY to match mapPointToScreen

* Add id and styling

* Run prettier

* Set z-index to 999

* Draw the label

* Introduce the centroid SVG, refactor code to allow both SVG layers

* Add text label and compute radius based on population

* Implement optional chaining

* Update font family

* Optimize calcMeanCentroid()

* Create and utilize calcMedianCentroid()

* Remove mass circle from label

* Remove styling change on hover

* Remove reducer action logs

* Prettier

* Swap out binds for arrow functions

* Style text

* switch from selectAll() to select()

* Reflect centroid container's purpose in id

* Remove mass from the output

* Swap to obj

* Add finite check

* Don't draw centroid if no finite values

* Fix finite check

* Remove log

* Toggle label coloring based on colorBy state

* Pass cursor events through centroid svg
2019-06-13 15:40:57 -07:00
Colin Megill 6aeefb0fe6 menubar (#804)
* menubar 1

* zoom switching

* centering, pixel perfect canvas

* remove dead args and code

* clipping

* remove log

* if

* connect props

* lint

* undo

* logo left, componetize

* graph back to full height

* shadow to top

* do not prematurely call event handlers during render

* change test to deal with async histogram creation

* left section padding

* lint

* adjust graph to account for top bar,

* lasso tests

* refine histogram tests

* remove testing (onlys)
2019-06-13 15:15:43 -07:00
Charlotte Weaver eac514e04d update favicon (#814) 2019-06-13 11:29:27 -07:00
Justin KigginsandCharlotte Weaver 9f9393a486 adds section on risks of hosted instances (#807)
Co-Authored-By: Charlotte Weaver <charlottesweaver@gmail.com>
2019-06-04 09:16:11 -07:00
Charlotte Weaver 1d6bb032a3 remove async from describe blocks (#805) 2019-06-03 14:59:16 -07:00
Bruce Martin ca9a6796d8 release 0.10.1 (#797) 2019-05-30 13:44:42 -07:00
Bruce Martin a6142bdf93 improve graph scale and centering (#796)
* add gutter to embedding canvas

* improve layout scale and translate

* fix lint

* pin tables to version 3.5.1

* fix lasso coordinate smoke tests
2019-05-30 13:31:41 -07:00
Bruce Martin c6252825f3 release 0.10.0 (#794) 2019-05-29 16:55:43 -07:00
Colin Megill 862d8feb5e x (#792) 2019-05-29 12:23:30 -04:00
Bruce Martin 1ef77d1596 fix misconfiguration for history management (#787) 2019-05-24 21:01:11 -07:00
Bruce Martin 3dc45d6330 do not hard-wire column names in annotations (#785)
* enforce column name uniqueness for obs and var

* parameterize the column name containing obs and var user-readable names

* use the new annotation index value from schema

* update f/e unit tests

* PR review suggestions

* lint
2019-05-24 21:00:54 -07:00
Bruce Martin e941c1a496 scaling omitted from event handlers (#789)
* scaling omitted from event handlers

* fix smoke tests
2019-05-24 07:00:04 -07:00
Colin Megill a657eb3152 Logo (#782)
* logo, black

* fixes

* remove template, move header
2019-05-23 11:47:24 -04:00
Bruce Martin ef7c26e799 correctly handle selection of trunctated categories (#781) 2019-05-23 08:46:22 -07:00
Bruce Martin 49af278de7 cleanup memoiziation in graph component (#783) 2019-05-22 17:37:18 -07:00
Bruce Martin 2357d0c1b8 layout change UI (#776)
* add layout to schema

* add layout choice action and reducer

* multi layout UI

* update unit tests

* add missing file

* update test schema

* fix duplicate test id

* fix tabs

* PR lint

* fix pytest
2019-05-22 13:21:33 -07:00
Bruce Martin fcc05f6a00 coordinate system fixes for embedded graph (#768)
* change pan speed to 1 per issue #722

* correct handle scaling of graph when aspect ratio less than one

* add package lock

* add invert to our scale functions

* correctly transform to/from gl coordinates

* remove unused import

* fix naming of import

* update smoke tests
2019-05-20 14:22:41 -07:00
Bruce Martin de3407d875 change scripts to support windows (#775) 2019-05-20 11:42:57 -07:00
Charlotte Weaver 2d4e827bea wait for element before getting text/html (#777) 2019-05-20 11:35:53 -07:00
Bruce Martin 1fa4838863 npm (js) package dependency updates (#765)
* JS package dependency updates

* additional package updates

* more package version updates

* more js package updates

* more JS dependency updates
2019-05-20 10:11:49 -07:00
Bruce Martin efa1709158 add multi-layout support to back-end (#766)
* add multi-layout support to back-end

* remove obsolete code

* temporary code to apply heuristic choice of default layout

* fix tests

* update python tests

* more py lint

* PR review changes

* more PR lint

* PR lint
2019-05-16 14:49:22 -07:00
Bruce Martin 7adac5d004 create occupancy stacks for all category values, not just top N values (#764) 2019-05-13 11:22:46 -07:00
Charlotte Weaver d522cc8f91 Add clipping test to smoke tests (#757)
* Add clipping test to smoke tests

* devtools on in debug
2019-05-09 15:31:55 -07:00