Monocle3 plotCells (version 0.1.5+galaxy1)

Input object in RDS format:

Format of input object:

The column of reducedDimS(cds) to plot on the horizontal axis.:

The column of reducedDimS(cds) to plot on the vertical axis.:

The dimensionality reduction for plotting.:

The cell attribute (e.g. the column of pData(cds)) to map to each cell's color, or one of {cluster, partition, pseudotime}.:

A list of gene IDs/short names to plot.:

For adding more than one gene, write them as a comma separated list, with no spaces in the middle, like `crp1,crp2,cycX`.

Determines how to transform expression values for plotting.:

The size of the point for each cell.:

The alpha aesthetics for the original cell points, useful to highlight the learned principal graph.:

If set, display the cell group names directly on the plot. Otherwise include a color legend on the side of the plot.:

When this option is set, skip displaying the trajectory graph inferred by learn_graph().:

If set, and setting --color-cells-by to something other than cluster, label the cells of each cluster independently. Can result in duplicate labels being present in the manifold.:

If set, label the leaves of the principal graph.:

If set, label the roots of the principal graph.:

If set, label the branch points of the principal graph.:

Emit verbose output:

Monocle3 cell plotting (plot_cells)

Display various information about cells (clustering, pseudotime, the inferred graph, user-provided annotations, gene expression) in reduced dimensions.

More information can be found at https://cole-trapnell-lab.github.io/monocle3/ and https://github.com/ebi-gene-expression-group/monocle-scripts

Version history 0.1.5+galaxy1: Updated to monocle3-cli 0.0.9 for plot cells to allow for multiple genes plotting.

0.1.5+galaxy0: Updated to monocle3-cli 0.0.8 to add top marker genes and fix container plots for plotCells (only those two modules upgraded).

0.1.4+galaxy0: Updated to monocle3-cli 0.0.7 to fix bug with column headers in tsv.

0.1.3+galaxy0: Updated to monocle3-cli 0.0.5 to fix bug with tsv inputs.

0.1.2+galaxy0: Initial version based on monocle3-cli 0.0.3 and monocle3 0.1.2