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Changelog

Source: NEWS.md

MCView 0.2.54

  • Switched serialization from qs to qs2 (qs was removed from CRAN). New cache files are saved in .qs2 format. Existing projects with .qs cache files are still supported via the legacy qs package (installed from GitHub).

MCView 0.2.53

  • Fix: stroke was not working in the atlas tab.
  • Fix: “Gene”, “Gene module” and “Metadata” selectors were not working in the atlas tab.

MCView 0.2.52

  • Fix: ‘s’ was considered as a new line character in gene list input in the ‘Gene correlation’ tab.

MCView 0.2.51

  • Added categorical filtering to the Markers tab.
  • Added sina/violin plots to the Cell types tab and added the option to set x axis to categorical metadata.
  • Added facets to the Cell types tab.

MCView 0.2.50

  • Added “Gene correlation” tab.

MCView 0.2.49

  • Added “Apply” button (and apply behaviour) to the ‘Markers’ tab.

MCView 0.2.48

  • Added controls for plotly download format, width, height and scale.
  • Fix: new cell types loaded from annotation file were not updated in all tabs.

MCView 0.2.47

  • Fix: diff. expr. crashed when comparing metacells.

MCView 0.2.46

  • Added “Move up” and “Move down” buttons to the ‘Cell types’ tab.
  • Added “Random seed” input to the ‘Manifold’ tab.

MCView 0.2.45

  • Reorder boxplot in cell types tab by cell type colors table.
  • Added “Show correlations” button, and compute correlation based on selected cell types in the ‘Cell types’ tab.

MCView 0.2.44

  • Added “Use DE genes” button to the ‘Markers’ tab, that uses the significantly differentially expressed genes from the ‘Diff. Expr.’ tab.

MCView 0.2.43

  • Added “Highlight selected genes” option to the ‘Markers’ tab.
  • Added help for the ‘Markers’ tab.
  • Fix: changing force_cell_type did not update the heatmap when in zoom mode.
  • Fix: show “Enrichment type” toggle when filtering by clipboard, and allow updating genes.
  • Added profiling mode for debug purposes.

MCView 0.2.42

  • Fix: apps did not start when light_version was TRUE.

MCView 0.2.41

  • Projects are now deployment-ready by default. An app.R file is automatically added during dataset import.
  • Unified the project and bundle structures - no need for a separate bundle creation step for basic deployment.
  • Added “Download data” button.
  • Keep the creation command in the config directory.
  • Added copy_source_file parameter to import_dataset to optionally copy the source h5ad file instead of creating a symlink.
  • Improved project directory handling with streamlined overwrite logic.
  • Added missing dataset name detection in import_dataset.

MCView 0.2.40

  • Show metadata in markers heatmap tooltip.
  • Added search to cell type selectors.
  • Reset on apply by default in Annotate tab.

MCView 0.2.39

  • Added log2 option to the scatter plots.
  • Fix: ‘Stroke’ was not working in the 2D projection plots.

MCView 0.2.38

  • Show GeneCards buttons also when Show-Correlations is off.

MCView 0.2.36

  • Fix: Metadata/Gene correlations were not shown.

MCView 0.2.35

  • Changed default of ‘Show correlations’ to FALSE.

MCView 0.2.34

  • Added an option to view corrected gene expression in the ‘Genes’ tab (discussion #170).
  • Added cell type selectors to the ‘Annotate’ tab.
  • Turn off the correlations on the ‘Genes’ tab by default when selecting a subset of the cell types.

MCView 0.2.33

  • Added cell type selector to the ‘Genes’ tab.
  • Added correlation between the genes/metadata shown in the ‘Genes’ tab.
  • Fix: rescale metadata colors on zoom in ‘Markers’ tab.
  • Fix: Adding new cell type prevented the use of diff. expression tab.
  • Disabled ‘select all’ in ‘Markers’ gene selector.

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

MCView 0.2.0

  • First stable version.