About

MCView

MCView creates a shiny-app facilitating interactive exploration and annotation of metacell models. Metacell itself is described here.

See more about MCView here, report a bug here.

Where to start

On the left sidebar you will find a list of tabs, click on the tab to open it. See below a short description of each tab.

Additional tabs can be added from the right sidebar which can be opened by clicking on the “Gears” icon at the top right of the screen. Select the tabs you want and then click on “Update Tabs”.

Tabs

Main tabs:

  • QC: View QC metrics of the metacell model.
  • Manifold: View the 2d projection of the manifold
  • Genes: Compare gene expression and metadata over the metacells.
  • Diff expression: Compare metacells / cell types.
  • Markers: View a heatmap of ‘marker genes’ over the metacell model.
  • Cell types: View gene expression and metadata over cell types.
  • Annotate: Assign cell types and colors to metacells.
  • Gene modules: Create gene modules to be used in other tabs.

QC tabs:

  • Inner-fold
  • Outliers

Atlas projection tabs:

  • Query: Examine the results of a projection of the metacell model over an atlas.
  • Atlas: View the 2d projection of the atlas.
  • Projected-fold

Additional tabs:

  • Samples

# of UMIs per metacell

Max inner-fold per metacell

# of metacells with significant inner-fold

Max inner-stdev per metacell

# of cells per metacell

Max zero-fold per metacell

# of cells with zero UMIs per gene

Type Projections

Projected correlation per metacell

Fitted genes per cell type

2D Projection

Modify colors

Gene/Gene

Select axes


Gene projections

Modify colors

Markers Heatmap

  • to

Diff. Expression

2D Projection

Cell types

Advanced Options


Plot Controls:
• Plot type affects visualization
• Faceting splits into panels
• Flip coords for long labels
• Y limits in plot sidebar

2D Projection

Gene/Gene


Differential expression


Metacell annotation

Cell Types



Inner-Fold Heatmap

  • to

Stdev-fold Heatmap

  • to

Outliers Heatmap

  • to

Vein plot

Genes Trajectory

Metacell flow

Sample types

Order by

Sample/Sample

Select axes

Sample projections

Query 2D Projection

Diff. Expression

Type Projections

Gene Observed / Projected

Gene metadata

Atlas 2D Projection

Gene Input




Find genes correlated with each input gene separately
Calculate correlations between the input genes (all correlations shown, filters disabled)
Treat genes as a module and find genes correlated with the combined expression




Correlation Heatmap

Top Correlations

Instructions



How to use:

1. Enter gene names in the text area (one per line)

2. Choose correlation mode (individual vs module)

3. Adjust parameters as needed

4. Click 'Calculate Correlations' to generate results


Visualizations will appear here after calculation.

Correlation Results


Results will appear here after calculation.