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MCGraphs - Generate graphs for visualizing scRNA-seq metacells data in a Daf data set.

Motivation

The goals of this are:

  • Provide a specific set of graphs allowing for investigation and visualization of the Metacells.jl data stored in Daf.jl.
  • Generate static PNG and/or SVG files (for publishing).
  • Generate interactive graphs in Jupyter notebook, both from Python and from R (for exploration).
  • Provide guided UI in Jupyter notebook for accessing and customizing the graphs, as well as generating standard dashboards of related graphs.
  • Be reasonably efficient when the data is large.
  • Be separated from the Metacells package itself, so people only doing computations will not be forced to bring in the plotting packages as dependencies.

If/when this is mature, this should replace MCView. Right now this is very much WIP. See the v0.1.0 documentation for details.

Architecture

The overall architecture of the solution is based on the following layered implementation:

Julia code:

  • Validations contains functions for validating user input which can be invoked by the UI to ensure valid inputs.
  • Renderers contains functions that actually render graphs, given the graph data and configuration. Each basic graph type has its own specification for the data and for the configuration. For example, a scatter plot data contains x coordinates, y coordinates, and colors, while the configuration controls the graph size, point shape and size, axis and graph titles, etc. We render most graphs using Plotly, but use ClusterGrammer2 for heatmaps.
  • Extractors contains functions that extract graph data from a Daf data set. For example, a gene-gene plot will extract the expression of two genes in all metacells as the x and y coordinates, colored according to the type of the metacells.
  • Plotters contains functions that combine extraction and rendering, that is, will render a graph given a Daf data set and a graph configuration. Each plot can specify different defaults for the graph configuration. For example, the default titles of a gene-gene plot would be different from the default titles of a differential expression plot, even though both will use the same scatter plot renderer.

Jupyter notebook code (need to be implemented in all Jupyter languages, requiring TODO: separate MCGraphs.py and MCGraphs.r packages):

  • Controllers are Jupyter notebook UI elements for specifying which data to extract for a graph, or the configuration of a graph. For example, a data controller for a gene-gene plot will allow selecting the two genes, and a configuration controller for a scatter plot graph will allow specifying the point shape and size.
  • Widgets combine multiple controllers to fully specify a graph to render. For example, a gene-gene graph widget will combine both the gene-gene plot data selection with the scatter plot graph configuration, using the specific defaults of the gene-gene graph.
  • Menus allow selecting a single widget (for rendering a single graph) or several related widgets (for rendering a standard dashboard of graphs). For example, one entry in a menu could be "gene-gene plot" which generates a single graph while another might be "metacells QC dashboard" which generates multiple graphs visualizing various metacells QC measures. Menus are nested in a tree, such that invoking the root menu allows the user to interactively navigate to any of the provided plots and dashboards, without having to memorize the function names and configuration options.

Generating graphs is in general a read-only operation, allowing the analyst to explore the data. However, some work flows require creating and modifying data, for example, manual metacells type annotations. This is supported by dedicated controllers that write data back into the Daf data set, which is typically a chain consisting of a large read-only base data set combined with a small writeable data set containing the manually entered data. This allows reusing the same base data set with multiple alternative manual annotations.

While the overall architecture of the code here generalizes well, the functionality here is intentionally restricted to what we found useful for visualizing scRNA-seq metacells data in Daf data sets. Likewise, the amount of customization of the graphs is intentionally limited. The intent here is to make it as easy as possible for the analyst working in Jupyter notebook to explore the data, and generate graphs for academic papers, not to create yet another end-all-be-all graphs framework (of which there are too many already).

Installation

Just Pkg.add("MCGraphs"), like installing any other Julia package. However, if being used in Jupyter notebook, you will probably want to install the language specific package instead:

TODO: To install the Python wrappers...

TODO: To install the R wrappers...

Features list:

This also serves as the main TODO list (including the Python and R wrappers).

Environment:

  • Static file Plotly graphs (Julia; TODO: Python, TODO: R).
  • Static file Heatmap graphs (TODO: Julia; TODO: Python, TODO: R).
  • Interactive Plotly graphs (TODO: Julia; TODO: Python, TODO: R).
  • Interactive Heatmap graphs (TODO: Julia; TODO: Python, TODO: R).
  • TODO: Jupyter notebook vs. Jupyter lab vs. REPL.

Graph types:

  • Distribution graph (Julia; TODO: Python, TODO: R).

    • Box graph.
    • Violin graph.
    • Curve graph.
    • Violin + Box graph.
    • Curve + Box graph.
    • Horizontal graph.
    • Log axis.

  • Distributions graph (Julia; TODO: Python, TODO: R).

    • Legend.
    • Separate.
    • TODO: Overlay.

  • Points graph (Julia; TODO: Python, TODO: R).

    • Diagonal bands (lines and fill).

    • Horizontal bands (lines and fill).

    • Vertical bands (lines and fill).

    • Color scale.

      • Named.
      • Reversed.
      • Manual.
      • Categorical.

    • Colorbar.

    • Borders.

      • Colorbar.

    • Edges.

    • Log axis.

  • Line graph (Julia; TODO: Python, TODO: R).

    • Horizontal bands (lines and fill).
    • Vertical bands (lines and fill).
    • CDF variant.

  • Lines graph (Julia; TODO: Python, TODO: R).

    • Legend.
    • Overlay.
    • Stacked.
    • CDFs variant.

  • Bar graph (Julia; TODO: Python, TODO: R).

  • Bars graph (Julia; TODO: Python, TODO: R).

    • TODO: Annotations.
    • TODO: Annotations Legend.

  • Heatmap graph (TODO: Julia; TODO: Python, TODO: R).

    • TODO: Annotations.
    • TODO: Tree.

  • Flow (Sankey) graph (TODO: Julia; TODO: Python, TODO: R).

Controllers:

  • Distribution controller (TODO: Julia; TODO: Python, TODO: R).

  • Distributions controller (TODO: Julia; TODO: Python, TODO: R).

  • Points controller (TODO: Julia; TODO: Python, TODO: R).

    • TODO: With border (TODO: Julia; TODO: Python, TODO: R).
    • TODO: With edges (TODO: Julia; TODO: Python, TODO: R).

  • Line controller (TODO: Julia; TODO: Python, TODO: R).

  • Lines controller (TODO: Julia; TODO: Python, TODO: R).

  • Bar controller (TODO: Julia; TODO: Python, TODO: R).

  • Bars controller (TODO: Julia; TODO: Python, TODO: R).

  • Heatmap controller (TODO: Julia; TODO: Python, TODO: R).

Widgets & Extractors & Plotters

  • UMIs/metacell distribution (TODO: Julia; TODO: Python, TODO: R).
  • Cells/metacell distribution (TODO: Julia; TODO: Python, TODO: R).
  • Max-inner-fold/metacell distribution (TODO: Julia; TODO: Python, TODO: R).
  • Max-inner-stdev/metacell distribution (TODO: Julia; TODO: Python, TODO: R).
  • Max-zero-fold/metacell distribution (TODO: Julia; TODO: Python, TODO: R).
  • Gene expression/cell type distributions (TODO: Julia; TODO: Python, TODO: R).
  • Projection correlation/metacells distribution (TODO: Julia; TODO: Python, TODO: R).
  • Gene/gene expression points (TODO: Julia; TODO: Python, TODO: R).
  • Genes significant inner-fold/expression points (TODO: Julia; TODO: Python, TODO: R).
  • Genes zero cells/expected points (TODO: Julia; TODO: Python, TODO: R).
  • Manifold points & edges (TODO: Julia; TODO: Python, TODO: R).
  • Differential expression points (TODO: Julia; TODO: Python, TODO: R).
  • Gene observed/projected points (TODO: Julia; TODO: Python, TODO: R).
  • Gene projection correction/expression points (TODO: Julia; TODO: Python, TODO: R).
  • Markers heatmap (TODO: Julia; TODO: Python, TODO: R).
  • Gene modules heatmap (TODO: Julia; TODO: Python, TODO: R).
  • Inner-fold heatmap (TODO: Julia; TODO: Python, TODO: R).
  • Stdev-fold heatmap (TODO: Julia; TODO: Python, TODO: R).
  • Projected-fold heatmap (TODO: Julia; TODO: Python, TODO: R).
  • Projection types stacked bars (TODO: Julia; TODO: Python, TODO: R).
  • Projection types fitted genes (TODO: Julia; TODO: Python, TODO: R).

Dashboards

  • Atlas Overview (TODO: Julia; TODO: Python, TODO: R).
  • Metacells QC (TODO: Julia; TODO: Python, TODO: R).
  • Projection QC (TODO: Julia; TODO: Python, TODO: R).
  • Annotation QC (TODO: Julia; TODO: Python, TODO: R).

Work flows

  • Compute metacells (TODO: Julia; TODO: Python, TODO: R).
  • Manual type annotations (TODO: Julia; TODO: Python, TODO: R).

License (MIT)

Copyright © 2024 Weizmann Institute of Science

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.