Galaxy |

Seurat Plot dimension reduction (version 4.0.4+galaxy0)

Choose the format of the input:

Seurat RDS, Seurat H5, Single Cell Experiment RDS, Loom or AnnData

RDS file:

Select RDS file(s) with Seurat object for input

Dimensionality reduction:

Which dimensionality reduction to use. Default is "pca", can also be "tsne", or "ica", assuming these are precomputed

X axis dimension:

Dimension for x-axis

Y axis dimension:

Dimension for y-axis

Cells list:

File to be used to derive a vector of cells to plot (default is all cells)

Point size:

Adjust point size for plotting

Label size:

Sets size of labels

Label clusters:

Repel labels:

Group by:

Group (color) cells in different ways

Colors:

Comma-separated list of colors, each color corresponds to an identity class. By default, ggplot assigns colors.

Cell attribute for shape:

If NULL, all points are circles (default). You can specify any cell attribute (that can be pulled with FetchData) allowing for both different colors and different shapes on cells.

Ident (clusters) order:

Comma-separated string specifying the order of plotting for the idents (clusters). This can be useful for crowded plots if points of interest are being buried. Provide either a full list of valid idents or a subset to be plotted last (on top).

Figure width:

Width of png in pixels.

Figure height:

Height of png in pixels.

What it does

Graphs the output of a dimensional reduction technique on a 2D scatter plot where each point is a cell and it's positioned based on the cell embeddings determined by the reduction technique. By default, cells are colored by their identity class (can be changed with the group.by parameter).

Seurat is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. It is developed and maintained by the Satija Lab at NYGC. Seurat aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data.

Inputs

Seurat RDS object

Outputs

PNG-format image file

Version history 4.0.0: Moves to Seurat 4.0.0, introducing a number of methods for merging datasets, plus the whole suite of Seurat plots. Pablo Moreno with funding from AstraZeneca.

3.2.3+galaxy0: Moves to Seurat 3.2.3 and introduce convert method, improving format interconversion support.

3.1.2_0.0.8: Update metadata parsing

3.1.1_0.0.7: Exposes perplexity and enables tab input.

3.1.1_0.0.6+galaxy0: Moved to Seurat 3.

Find clusters: removed dims-use, k-param, prune-snn.

2.3.1+galaxy0: Improved documentation and further exposition of all script's options. Pablo Moreno, Jonathan Manning and Ni Huang, Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/. Parts obtained from wrappers from Christophe Antoniewski (GitHub drosofff) and Lea Bellenger (GitHub bellenger-l).

0.0.1: Initial contribution. Maria Doyle (GitHub mblue9).