NEWS.md

In tanaylab/MCView: A Shiny App for Metacell Analysis

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

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

MCView 0.2.0

• First stable version.

tanaylab/MCView documentation built on June 1, 2025, 8:08 p.m.