Commit Graph
18 Commits
Author SHA1 Message Date
Sidney BellandMatt Weiden 9089fc98f2 annotations cli updates (#1190)
* Switch logic from `--annotations` to `--disable-annotations

* Rename `--annotations-file` --> `--annotations-input-file` and remove `experimental`

* update docs

* update makefile

* update tests

* Disable annotations on standard client smoke test

* Update docs/posts/annotations.md

Co-Authored-By: Matt Weiden <538456+mweiden@users.noreply.github.com>

* Update docs/posts/annotations.md

* Renaming

* Docs

* Update tests

* Pesky typo -_-

Co-authored-by: Matt Weiden <538456+mweiden@users.noreply.github.com>
2020-03-11 11:57:52 -07:00
Sidney Bell a927d733c2 [WIP] Patch for anndata 0.7 (#1132)
* Fix JSON encoding bug introduced by anndata 0.7

* Add anndata csr and csc classes to allowed matrix proxy inputs
2020-01-28 16:12:43 -08:00
Sidney Bell 2832393f40 Make diffexp docs more specific (#1083)
* Update diffexp docs w/ more explicit assumptions, etc.

* Minor edits

* Formatting and cross-checking with `diffexp.py`
2020-01-16 15:44:10 -08:00
Sidney Bell 97738e5c2d Remove FAQ link from info menu (#1084) 2020-01-02 16:04:38 -08:00
Sidney Bell ec79995be8 Reorganize annotations docs to emphasize hosted vs single-user modes (#1067) 2019-12-03 17:02:35 -08:00
Sidney Bell 9c09ee6329 Update readme and other repo MD files (#1063)
* Update readme

* Move roadmap to main docs site

* Avoid duplication by just putting a pointer to the actual docs
2019-11-26 16:09:59 -08:00
Sidney Bell 9bcafeb7c1 [WIP] Overhaul the documentation site (#1030)
Overhaul the whole documentation site
2019-11-22 14:54:20 -08:00
Sidney BellandSeveriano Badajoz f41f47cf1b Fix mistakenly removed badges (oops) (#955)
* Fix mistakenly removed badges (oops)

* Update README.md

Co-Authored-By: Severiano Badajoz <sbadajoz@chanzuckerberg.com>
2019-09-30 16:00:29 -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
Sidney Bell 98b07b1284 Add code of conduct; move contributing guidelines to CONTRIBUTING.md (#842) 2019-07-11 10:09:35 -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
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
Sidney Bell 34e5a91dc6 Add calculate_qc_metrics to `prepare (#697)
* Calculate QC metrics

* Add QC metrics to prepare section of readme

* Add pointer to scanpy qc metrics function

* Don't explicitly pass qc flag as arg

* Add explicit toggle for run-qc/skip-qc

* Move qc metrics calculation to separate step/function
2019-04-09 08:56:07 -07:00
Sidney Bell c9a56fa73a Update scanpy version (#688)
Update to version 1.3.7
2019-04-04 12:16:30 -07:00
Sidney Bell 16f93397ae Support diffmap and phate layouts. Explicitly handle embeddings with >2 components. (#662)
* Add diffmap and phate to supported embeddings

* Explicitly pull the first two components of any given layout
2019-03-21 19:06:05 -07:00
Sidney Bell b6f946ec8a Add note about installing hdf5 to FAQ (#581) 2019-02-08 14:56:16 -08:00
Sidney Bell 77ca5c267e Update readme (#137)
* Update readme

* Add demo gif

* Update README.md

* Update README.md

* Update README.md

* Update README.md

* Update README.md
2018-08-03 10:23:57 -07:00