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NEWS.md

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MCView 0.2.32

  • Search genes by startsWith instead of contains.
  • Slightly larger default point size in gene/gene plots.
  • Do not show cell types with no metacells in the 'Markers' tab (issue #161).

MCView 0.2.31

  • Do not reorder tabs when they are set in the config file.

MCView 0.2.30

  • Added an option to include metadata when downloading marker heatmap.

MCView 0.2.29

  • Added "Enrichment type" toggle to the 'Markers' tab.

MCView 0.2.28

  • Added an option to show only fitted genes in the projected fold tab.
  • Moved "Order by" and "Force cell type" to left sidebar in the 'Markers' tab.
  • Added "Order cell types by" option to the 'Markers' tab.
  • Fix: legend did not appear in the 'Markers' tab when using ggplot 3.5.0.

MCView 0.2.27

  • Added an option to order by metadata when 'force cell type' is FALSE.
  • Added lateral/noisy labels to gene selectors.

MCView 0.2.26

  • Multiple fixes:
  • Fix: loading of light_version bundles was broken.
  • Fix: projection_point_size and scatters_point_size were not detected when added in other_params.
  • Fix: import warned when there were metacells withour an edge when providing default_graph parameter.
  • About tab is now the first in light-version bundles.

MCView 0.2.25

  • Added an option to exclude lateral and noisy genes from marker heatmap.

MCView 0.2.24

  • Added 'Load genes' and 'Save genes' buttons to the 'Markers' tab.
  • Added 'Top correlated' widgets to metadata and gene modules.
  • Added some missing package imports.

MCView 0.2.23

  • Fix: plot limits were sometimes too low in differential expression plots.

MCView 0.2.22

  • Added an option to sort gene heatmaps by metadata within each cell type.
  • In 'Projection QC' tab, changed percentage of 'similar' to percentage of 'dissimilar' metacells.

MCView 0.2.21

  • Fixed gene name colors in the 'Gene modules' tab.

MCView 0.2.20

  • Fixed metadata colors at 2D projections (previously the breaks were simply ignored)

MCView 0.2.19

  • Added an option to use disk for shiny caching (see shiny_cache_dir and shiny_cache_max_size parameters in create_bundle)
  • Fix: sidebar still showed spaces for excluded tabs.

MCView 0.2.18

  • Added 'overwrite' parameter to import_dataset.
  • Fixed an edge case in which a cell type was not continuous in the markers heatmap order.

MCView 0.2.17

  • Fix: atlas tab was not working after the new UMAP feature.
  • Use corrected expression in the differential expression in the Query tab.
  • Mark dissimilar metacells in metacell selectors.

MCView 0.2.16

  • Added gene colors legend to the 'Markers' tab.

MCView 0.2.15

  • Added 'any' cell type to gene metadata table at Query tab.
  • Added a value box with % of fitted genes out of atlas markers.

MCView 0.2.14

  • Query tab improvements: added a correction factor line and an option to show only fitted genes.

MCView 0.2.13

  • Added UMAP computation given anchor genes to the 'Manifold' tab.

MCView 0.2.12

  • Added Sample types plot to the Samples tab.
  • Fixed a few bugs in the Samples tab.

MCView 0.2.11

  • Fix: fitted gene plot was not shown when 'corrected_factor' was missing from the input data.

MCView 0.2.10

  • Changed zero-fold per gene plot to show expression vs zero-fold.
  • Added two static plots to About tab.
  • Added "top-correlated" panel to "Cell types" tab.
  • Added "inner-std" plot to QC panel.
  • Added "Stdev-fold" tab.
  • Added "Projection QC" tab
  • Fix: differential expression between metacells did not work with most recent version of qs.
  • Added Lasso selection in Annotation and Differential Expression tabs.
  • Added "# of metacells with significant inner-fold" to the "QC" tab.
  • Filter lateral/noisy genes from diff expression plots.
  • Annotate genes with their lateral/noisy status + gene modules.

MCView 0.2.9

  • Fixed import according to newest metacells version.

MCView 0.2.8

  • Added the 'QC' tab. Please re-import your dataset in order to enable it.
  • Moved some of 'gene/gene' and 'projection' controls to below the plot.
  • Added 'excluded_tabs' to the config file.
  • Added a footer with MCView and metacells versions.
  • Some modifications to the 'Genes' tab layout.
  • Added an option to color the 2D projection by an axis from the Gene/Gene plot.

MCView 0.2.7

  • Added QC metrics to the manifold tab.
  • Fix: import_cell_metadata was overwriting existing metadata
  • Fix: import crashed when metacell_types had missing colors

MCView 0.2.6

  • Use new metacells version. Note that old anndata objects will not work with this version without conversion.
  • Added an option to bundle a 'light' version without the option to change the genes on heatmaps.
  • Fixed resolution of heatmap plots.
  • Added a 'rename' modal to the 'Annotate' tab.
  • Fixed order of negative correlations in the left panels. Fixes #127.
  • Added an option to use 'gene_names' parameter with atlas projection.
  • Use the name of the dataset as title by default.
  • Rasterized Type Prediction plot.

MCView 0.2.5

  • Added tab selector.
  • Runtime optimizations: load tabs only on click.
  • Some css fixes.
  • Changed default 'about' document.
  • Added preloader spinner.
  • Allow using run_app with the bundle folder.
  • Added cell metadata support for metacell1 import.
  • Fix: clicking on a cell type on the manifold legend was sometimes not aligned with the gene/gene plot.
  • Fix: categorical metadata tooltip was wrong in projection plots.
  • Changed metacell selectors to search with "contains" instead of "startWith" behaviour.

MCView 0.2.4

  • Add an option to add metacells to clipboard by number
  • runtime optimizations: use virtualSelectInput

MCView 0.2.3

  • Added support for gene modules ('Gene modules' tab).
  • Added 'Outliers' tab.
  • Added Clipboard functionality.
  • Added support for alternative gene names.
  • Added control over the number of clusters / whether to cluster at all in the import phase.
  • Added new selection controls to Annotate tab ('Gears' symbol on the upper right of 'Metacell Annotation' box).
  • Bug fix: heatmaps crashed when only a single gene was chosen.
  • Bug fix: automatically color cell types missing from cell type colors file.
  • Bug fix: Diff expr. crashed when there was only a single cell type.
  • Bug fix: Wrong tooltip in metadata/metadata scatter plot.
  • Bug fix: Annotation colors in markers heatmap were scaled relative to current zoom.
  • Added control for marker selection parameters in import_dataset.

MCView 0.2.2

  • Added support for atlas projections ('Atlas', 'Query' and 'Projected-fold' tabs)
  • Added tooltip and interactive clicks to heatmaps ('Markers' and 'Projected-fold' tabs)
  • Added zoom for heatmaps.
  • Homogenize Annotate, Diff. Expr and Genes tabs.
  • Added 'Cell types' tab.
  • Added support for cell metadata using the 'Samples' tab.
  • Allow coloring by categorical metadata annotations.
  • Moved flow graphs to their own tab named 'Flow'.
  • create_project and import_dataset now accept the config file parameters.
  • Added option to force x and y limits to be the same in gene/gene plots.
  • Added an option to show x=y line in gene/gene plots.

MCView 0.2.1

  • Added Metadata tab.
  • Added Markers tab.
  • Added inner-fold matrix to markers tab.
  • Added an option to compare cell types on Metacell tab.
  • Added a download button.
  • Added a busy spinner.
  • create_project now only takes a path (instead of path + project name)
  • implicitly create a project when importing
  • import cell type annotation using a single file that contains both metacell types and cell type colors.
  • Bug fixes: issues #48, #51, #52, #60, #62 and more.
  • Changed gene selectors on the manifold tab to be on-demand (to reduce initialization time).
  • Added (some) caching.

MCView 0.2.1

  • A few bug fixes. See issues #36, #37, #38, #40, #41 and #42.

MCView 0.2.0

  • First stable version.