| 5c15aa1 | Gökçen Eraslan | 24 August 2020, 18:23:32 UTC | Use iloc for positional slicing in HVG (#1389) | 24 August 2020, 18:23:32 UTC |
| 912e7d0 | Philipp A | 24 August 2020, 14:37:42 UTC | Centralize setup information (#1381) | 24 August 2020, 14:37:42 UTC |
| c9fbe5c | Gökçen Eraslan | 20 August 2020, 22:41:32 UTC | Fix values_to_plot literal (#1384) | 20 August 2020, 22:41:32 UTC |
| 25836d1 | Isaac Virshup | 19 August 2020, 12:03:09 UTC | Temporarily revert flit commits (#1380) This reverts commits: f2efd3ad27ae7c461da2ef5dcd8a6129cd91ca19 4e9496baad3edac7243a0d62cb69a0dbd2b3f0e2 e06d921559b0aa15a9844c40ceb0d72a0ab0bc47 d66a5e4b9c816d526c939ef05b89d188fcfa1444 28aea53ac14e04d1683e6eda568b816977456b5a | 19 August 2020, 12:03:09 UTC |
| f2efd3a | Philipp A | 18 August 2020, 15:45:43 UTC | Add instructions for conda dev install (#1377) | 18 August 2020, 15:45:43 UTC |
| 4e9496b | Philipp A | 18 August 2020, 14:33:51 UTC | Allow JUST symlinking anndata installs (#1378) | 18 August 2020, 14:33:51 UTC |
| e06d921 | Philipp A | 18 August 2020, 08:44:01 UTC | Fix install (#1376) | 18 August 2020, 08:44:01 UTC |
| d66a5e4 | Philipp A | 17 August 2020, 20:50:19 UTC | pytest can also be configured in TOML! (#1375) | 17 August 2020, 20:50:19 UTC |
| 28aea53 | Philipp A | 17 August 2020, 19:20:56 UTC | Switch to flit (#1374) | 17 August 2020, 19:20:56 UTC |
| 5533b64 | Philipp A | 16 August 2020, 20:21:03 UTC | short version of print_versions and print_header (#1373) | 16 August 2020, 20:21:03 UTC |
| 6c16f31 | Alex Wolf | 15 August 2020, 22:27:03 UTC | version 1.6.0 (#1372) * streamline release latest * further fixes | 15 August 2020, 22:27:03 UTC |
| 8611dba | stuartarchibald | 07 August 2020, 13:43:46 UTC | Promote ns from machine int to int64. (#1359) Co-authored-by: Philipp A <flying-sheep@web.de> | 07 August 2020, 13:43:46 UTC |
| 090d577 | Chris Rands | 05 August 2020, 19:57:51 UTC | A few minor style changes via `pyupgrade` (#971) Co-authored-by: Philipp A <flying-sheep@web.de> | 05 August 2020, 19:57:51 UTC |
| f6212ce | Gökçen Eraslan | 01 August 2020, 19:41:24 UTC | Proper string comparison (#1350) | 01 August 2020, 19:41:24 UTC |
| e6474b5 | Joshua Gould | 01 August 2020, 18:52:26 UTC | added cirrocumulus (#1311) Co-authored-by: Gökçen Eraslan <gokcen.eraslan@gmail.com> | 01 August 2020, 18:52:26 UTC |
| b9f3257 | Philipp A | 01 August 2020, 13:40:45 UTC | `print_versions` outputs more, updated GH issue template (#1343) | 01 August 2020, 13:40:45 UTC |
| 2ea9f83 | Fidel Ramirez | 01 August 2020, 05:31:54 UTC | fix missing yticklabels (#1342) * fix missing yticklabels * added `yticklabels` parameter to `sc.pl.stacked_violin()`. * fixed problem with overlapping tick labels and legend * improved formatting of the tick labels | 01 August 2020, 05:31:54 UTC |
| 96bd59d | Philipp A | 31 July 2020, 15:28:28 UTC | Use theme from scanpydoc (#1349) | 31 July 2020, 15:28:28 UTC |
| 4856784 | Isaac Virshup | 31 July 2020, 09:52:47 UTC | Export concat (#1348) | 31 July 2020, 09:52:47 UTC |
| ab9247b | Isaac Virshup | 31 July 2020, 07:18:39 UTC | Shorten _download function | 31 July 2020, 07:54:32 UTC |
| 650c20d | Isaac Virshup | 30 July 2020, 09:19:24 UTC | Register internet test marker, gets rid of warnings | 31 July 2020, 07:54:32 UTC |
| 0da9559 | Isaac Virshup | 30 July 2020, 09:11:36 UTC | Update number of genes for test dataset | 31 July 2020, 07:54:32 UTC |
| 24f77fe | Isaac Virshup | 30 July 2020, 09:05:58 UTC | Rewrite _download As noted in #1334, visium downloads were broken. Setting a header on downloads seems to fix them. We can't use the solution suggested in #1334 since it modifies global state around `urllib`, which is asking for trouble. This unfortunatley means most of the method had to be reimplemeted. The new implementation is based on `urllib.requests.urlretrieve`, but with a modification to let us pass a header. I've also removed the automatic `mkdir(..., parents=True)` from `_download` since typos could result in very messy filesystems. | 31 July 2020, 07:54:32 UTC |
| fc01716 | Alex Wolf | 30 July 2020, 12:18:34 UTC | Organize news section (#1345) * briefer statement * add news file * less wordy * fix articles | 30 July 2020, 12:18:34 UTC |
| 2f160ea | Isaac Virshup | 30 July 2020, 06:16:09 UTC | Minor code cleanup for sc.pl.rank_genes_groups Mostly reducing flow control, moving similar statements together | 30 July 2020, 06:37:04 UTC |
| 4d08f5a | Isaac Virshup | 29 July 2020, 09:29:36 UTC | Update reference figures for tests | 30 July 2020, 06:37:04 UTC |
| 55a57db | Isaac Virshup | 29 July 2020, 07:42:59 UTC | Fix y-axis for rank_genes_groups * Previously min and max were set by full range of scores, not just the ones being plotted. * Also did some minor code simplification. | 30 July 2020, 06:37:04 UTC |
| dc70a14 | Koncopd | 29 July 2020, 20:26:34 UTC | expand test | 29 July 2020, 22:04:05 UTC |
| e95dbcf | Koncopd | 29 July 2020, 18:43:48 UTC | update release notes | 29 July 2020, 22:04:05 UTC |
| 182c245 | Rybakov | 23 July 2020, 14:58:03 UTC | fix test | 29 July 2020, 22:04:05 UTC |
| 29924bd | Rybakov | 23 July 2020, 12:55:11 UTC | test tie corrected pvals | 29 July 2020, 22:04:05 UTC |
| aefd687 | Rybakov | 23 July 2020, 12:19:45 UTC | default values for _RankGenes | 29 July 2020, 22:04:05 UTC |
| dda90b1 | Rybakov | 23 July 2020, 12:11:51 UTC | fix n_genes in correction | 29 July 2020, 22:04:05 UTC |
| 73d590a | Rybakov | 21 July 2020, 15:01:45 UTC | doc for tie_correct | 29 July 2020, 22:04:05 UTC |
| 846446e | Rybakov | 21 July 2020, 14:05:17 UTC | add tie correction | 29 July 2020, 22:04:05 UTC |
| cf98241 | Alex Wolf | 29 July 2020, 15:14:27 UTC | Clean up release notes for v1.6.0 (#1339) * clean up release notes * fix typo * add statement on original references * better wording | 29 July 2020, 15:14:27 UTC |
| d4d373e | Fidel Ramirez | 29 July 2020, 13:39:09 UTC | split BasePlot.show() into show and savefig to match matplotlib style (#1329) * separated functionality of BasePlot.show() as `savefig` and `show` which is more in-line with matplotlib way of working and modified visual parameters to avoid light colored elements to blend with background | 29 July 2020, 13:39:09 UTC |
| debf131 | Isaac Virshup | 29 July 2020, 05:50:31 UTC | Add hvg to release notes | 29 July 2020, 08:12:57 UTC |
| 4ef47fb | Isaac Virshup | 29 July 2020, 05:27:21 UTC | Update nonnegative integer check Minor update, just checking if the type is already an integer, and doing a faster check for positive values. | 29 July 2020, 08:12:57 UTC |
| c8be573 | adamgayoso | 30 June 2020, 05:40:01 UTC | fix nan handling | 29 July 2020, 08:12:57 UTC |
| 3b26ccf | adamgayoso | 30 June 2020, 05:20:54 UTC | better handle nan in merging hvgs in batches seurat v3 | 29 July 2020, 08:12:57 UTC |
| 5859327 | adamgayoso | 29 June 2020, 17:22:37 UTC | skmisc travis | 29 July 2020, 08:12:57 UTC |
| ce008b1 | adamgayoso | 29 June 2020, 16:52:07 UTC | gzip test file | 29 July 2020, 08:12:57 UTC |
| d091c82 | Isaac Virshup | 29 June 2020, 05:43:07 UTC | Fix formatting test | 29 July 2020, 08:12:57 UTC |
| 9a567be | adamgayoso | 17 June 2020, 18:17:19 UTC | update docstrings, uns key added, defaults | 29 July 2020, 08:12:57 UTC |
| c34b043 | adamgayoso | 17 June 2020, 18:07:09 UTC | add util test | 29 July 2020, 08:12:57 UTC |
| 0c0cc3a | adamgayoso | 17 June 2020, 06:37:53 UTC | fix merging with batch key, add batch test | 29 July 2020, 08:12:57 UTC |
| afa19d6 | adamgayoso | 16 June 2020, 22:47:13 UTC | fix plotting function | 29 July 2020, 08:12:57 UTC |
| fb63e4c | adamgayoso | 16 June 2020, 22:32:43 UTC | update check raw data util | 29 July 2020, 08:12:57 UTC |
| d79213f | adamgayoso | 16 June 2020, 22:25:16 UTC | update docstring again | 29 July 2020, 08:12:57 UTC |
| 8bae64a | adamgayoso | 16 June 2020, 22:16:36 UTC | update docstring | 29 July 2020, 08:12:57 UTC |
| 2a771a4 | adamgayoso | 16 June 2020, 22:09:49 UTC | plot function code readability | 29 July 2020, 08:12:57 UTC |
| 691ed9c | adamgayoso | 16 June 2020, 22:05:49 UTC | update plot function | 29 July 2020, 08:12:57 UTC |
| a4ad0a5 | adamgayoso | 16 June 2020, 20:41:17 UTC | fix layer option seurat v3 | 29 July 2020, 08:12:57 UTC |
| b7c7130 | adamgayoso | 16 June 2020, 20:24:02 UTC | add layer option, check nonnegative integers | 29 July 2020, 08:12:57 UTC |
| 04a28a9 | adamgayoso | 16 June 2020, 19:43:41 UTC | missed import init | 29 July 2020, 08:12:57 UTC |
| 5f8a1fe | adamgayoso | 16 June 2020, 19:37:20 UTC | initial move to a unified function | 29 July 2020, 08:12:57 UTC |
| ea4f632 | adamgayoso | 16 May 2020, 17:58:40 UTC | update test | 29 July 2020, 08:12:57 UTC |
| e6978de | adamgayoso | 29 June 2020, 17:16:33 UTC | update name, skmisc dependency, return, docstring cleanup | 29 July 2020, 08:12:57 UTC |
| e0b4432 | adamgayoso | 07 May 2020, 00:04:31 UTC | remove loess helper | 29 July 2020, 08:12:57 UTC |
| c4ab2e8 | adamgayoso | 06 May 2020, 23:31:11 UTC | use loess fitted values | 29 July 2020, 08:12:57 UTC |
| 1760b9d | adamgayoso | 06 May 2020, 18:33:13 UTC | fix test | 29 July 2020, 08:12:57 UTC |
| 748e4cb | adamgayoso | 29 June 2020, 17:14:12 UTC | implementation with skmisc loess and handling sparse | 29 July 2020, 08:12:57 UTC |
| 10937f5 | michalk8 | 27 July 2020, 08:24:09 UTC | Fix pl.paga with pie charts (#1123) * Add simpler version of piecharts for paga * Fix unused variable * Add check for sum * Add is_close instead of less than * Forgot not * Fix paga_pie, add options to use names in the mapping * Add nicer and stricter warning message, remove debugging print * Add test, update docstring * Remove unused vars Co-authored-by: Michal Klein <michal.klein@tngtech.com> Co-authored-by: Fidel Ramirez <fidel.ramirez@gmail.com> | 27 July 2020, 08:24:09 UTC |
| 3a6f301 | michalk8 | 22 July 2020, 13:28:55 UTC | Add ylabel option to violin (#1161) * Add ylabel option to violin | 22 July 2020, 13:28:55 UTC |
| e9f9de3 | Edward S. Rice | 21 July 2020, 20:45:44 UTC | Add support for Harmony integration (#1306) | 21 July 2020, 20:45:44 UTC |
| 7d58f79 | Isaac Virshup | 21 July 2020, 09:45:32 UTC | Format recipes | 21 July 2020, 11:05:08 UTC |
| 855d652 | Isaac Virshup | 21 July 2020, 09:43:38 UTC | Fix weinreb recipe + test Also moved some deprecated preprocessing methods from _simple to _deprecated | 21 July 2020, 11:05:08 UTC |
| f59ebb8 | Fidel Ramirez | 21 July 2020, 09:49:15 UTC | updated documentation to point to latest plotting tutorial (#1319) * updated documentation to point to latest plotting tutorial * added release notes * final touches to the release notes * fix link and old contributions * added bugfixes and other changes to the release notes * Fix problem breaking docs build. Co-authored-by: Alex Wolf <f.alex.wolf@gmx.de> | 21 July 2020, 09:49:15 UTC |
| ff2f039 | Philipp A | 20 July 2020, 15:00:35 UTC | Reduce error potential from networkx (e.g. #1227) (#1323) | 20 July 2020, 15:00:35 UTC |
| ea8dde9 | Koncopd | 07 July 2020, 20:24:58 UTC | fix dtype of names in test | 20 July 2020, 13:38:02 UTC |
| bd9980a | Koncopd | 07 July 2020, 19:11:05 UTC | avoid trimming of genes' names | 20 July 2020, 13:38:02 UTC |
| bba495a | Koncopd | 07 July 2020, 19:02:53 UTC | allow to recompute in _RankGenes | 20 July 2020, 13:38:02 UTC |
| 2394916 | Koncopd | 07 July 2020, 18:31:26 UTC | test wilcoxon symmetry | 20 July 2020, 13:38:02 UTC |
| 56fdeaa | Rybakov | 07 July 2020, 15:53:16 UTC | format | 20 July 2020, 13:38:02 UTC |
| 0120ada | Rybakov | 07 July 2020, 15:50:40 UTC | fix pvalues for wilcoxon | 20 July 2020, 13:38:02 UTC |
| 75d7e4c | Rybakov | 07 July 2020, 13:32:06 UTC | fix vstack | 20 July 2020, 13:38:02 UTC |
| 9920341 | Adam Gayoso | 17 July 2020, 08:40:03 UTC | add backup url option read_10x_h5 (#1296) Co-authored-by: Gökçen Eraslan <gokcen.eraslan@gmail.com> Co-authored-by: Isaac Virshup <ivirshup@gmail.com> | 17 July 2020, 08:40:03 UTC |
| dc884f2 | Isaac Virshup | 17 July 2020, 08:12:54 UTC | Make sure dependencies are up to date in travis builds (#1320) * Add explicit numpy dependency * Remove unneeded umap dependency for anndata-dev builds | 17 July 2020, 08:12:54 UTC |
| 136177f | michalk8 | 17 July 2020, 04:52:49 UTC | Add CellRank to Scanpy's ecosystem (#1304) | 17 July 2020, 04:52:49 UTC |
| 30285c1 | Nikolaos Papadopoulos | 14 July 2020, 08:01:20 UTC | Update installation.rst correct leidenalg package name | 14 July 2020, 08:48:27 UTC |
| 76e6b28 | giovp | 13 July 2020, 13:18:35 UTC | black | 14 July 2020, 05:53:15 UTC |
| 17eb933 | giovp | 13 July 2020, 12:47:47 UTC | add default test | 14 July 2020, 05:53:15 UTC |
| 76ee9a8 | giovp | 28 May 2020, 07:30:20 UTC | fix default size of spot | 14 July 2020, 05:53:15 UTC |
| 1a45e1c | Fidel Ramirez | 13 July 2020, 11:02:48 UTC | updated documentation images; fix style overwrite after multiple calls to style(); added padding parameter to style to address #1270; add legend width units to documentation. (#1316) | 13 July 2020, 11:02:48 UTC |
| 529336d | Fidel Ramirez | 10 July 2020, 11:04:10 UTC | Fix docs for new plotting classes (#1309) Co-authored-by: Philipp A <flying-sheep@web.de> | 10 July 2020, 11:04:10 UTC |
| c23baf3 | Alex Wolf | 02 July 2020, 17:26:07 UTC | Avoid warning in rank_genes_groups if 't-test' is passed (#1303) | 02 July 2020, 17:26:07 UTC |
| b910afc | Fidel Ramirez | 29 June 2020, 16:34:30 UTC | improvements on plotting functions that use 'groupby' (#1210) * Unifies common code between `dotplot`, `matrixplot` and `stacked_violin` plots while adding flexibility to the plots. sc.pl.dotplot`, `sc.pl.matrixplot` and `sc.pl.stacked_violin` methods had been transformed into wrappers for the new `DotPlot`, `MatrixPlot` and `StackedVioling` classes. Accessing the new classes directly allows further fine tuning of the plots. * The new plot classes are all descendants of `BasePlot` class that captures the common code. The design of the classes follows the method chaining (as found in Pandas or Altair). This allows the addition of independent features (via well documented methods) to the plot without increasing the number parameters of a single function. This was first suggested here #956. All objects have consistent functions for `legend`, to set up titles and width, `style()` to set visual parameters specific to each plot like colormap, edge color, linewidth. `swap_axes` to transpose the figure, `add_dendrogram` with options to change the with of the dendrogran and `add_total` tho show a bar plot of the total number of cells per category. Also includes options to sort the categories. * Previous functionality is maintained but plots will look slightly different. * This commit addresses issues from #979 and #1103 related to `sc.pl.dotplot` * Now is possible to plot fold changes, log fold changes and p-values from `sc.tl.rank_genes_groups` as suggested in #562 Specific changes: **all figures**: * Set a title to the image. * Pass an `axe` where to plot the image. * Return a dictionary of axes for further manipulation * using `return_fig` the plot object can be used to adjust the proportions to the legend and other visual aspects can be fine tuned. * a bar plot with the totals per category can be added. This will align at the left of the image if the categories are plotted in rows or at the top if they are plotted in columns. * legend can be removed * `groupby` can be a list of categories. **dotplot** * Improved the colorbar and size legend for dotplots. Now the colorbar and size have titles, which can be modified using the `colorbar_title` and `size_title` arguments. They also align at the bottom of the image and do not shrink if the dotplot image is smaller. * Plot genes in rows and categories in columns (swap_axes). * Using the DotPlot object the dot_edge_color and line width can be set up, a grid added as well as several other features * `sc.pl.rank_genes_groups_dotplot` can now plot `pvals` and `log fold changes` **matrixplot** * added title for colorbar and positioned as in dotplot * `sc.pl.rank_genes_groups_matrixplot` can now plot `pvals` and `log fold changes` **stacked_violin** * violin colors can be colored based on average gene expression as in dotplots * made the linewidth of the violin plots smaller. * removed the tics for the y axis as they tend to overlap with each other. Using the `style` method they can be visualized. **other** * `sc.pl.heatmap` and `sc.pl.trackplots` now return a dictionary of axes when `show=False` as for the other plots. * now 'interpolation' can be passed as parameter for `sc.pl.heatmap` | 29 June 2020, 16:34:30 UTC |
| a659085 | Isaac Virshup | 29 June 2020, 03:39:39 UTC | Restrict sphinx version to < 3.1, > 3.0 | 29 June 2020, 04:05:55 UTC |
| e4fe2dd | Koncopd | 23 June 2020, 14:51:16 UTC | fix dendrogram for scipy 1.5 | 23 June 2020, 15:37:22 UTC |
| be9ff54 | Koncopd | 23 June 2020, 13:36:55 UTC | clean _ranks | 23 June 2020, 15:37:22 UTC |
| 8384401 | Rybakov | 16 June 2020, 15:23:00 UTC | rm ns | 16 June 2020, 15:42:52 UTC |
| 49235c3 | Rybakov | 16 June 2020, 12:18:34 UTC | clean n_genes defaults | 16 June 2020, 15:42:52 UTC |
| f852e5f | Koncopd | 10 June 2020, 08:17:42 UTC | eliminate zeros for sparse | 16 June 2020, 15:42:52 UTC |
| ffe2d79 | Koncopd | 05 June 2020, 21:14:07 UTC | docs | 16 June 2020, 15:42:52 UTC |
| a833dce | Koncopd | 05 June 2020, 20:40:19 UTC | format | 16 June 2020, 15:42:52 UTC |
| 1cf5287 | Koncopd | 05 June 2020, 20:35:15 UTC | standard output | 16 June 2020, 15:42:52 UTC |
| 5507dc3 | Koncopd | 31 May 2020, 21:11:31 UTC | no yield in _basic_stats | 16 June 2020, 15:42:52 UTC |
| 97fd3bf | Koncopd | 31 May 2020, 20:04:26 UTC | clean and fix | 16 June 2020, 15:42:52 UTC |
| 457f31d | Koncopd | 31 May 2020, 19:36:10 UTC | don't compute pts by default | 16 June 2020, 15:42:52 UTC |
