Description Usage Arguments Value Note Examples

schematize a sequence of projection methods

1 | ```
defaultProjectors(warmdim = 15)
``` |

`warmdim` |
numeric(1) defaults to 15 – defines the dimension reduction using irlba()$u for 'warming up' prior to UMAP or t-SNE runs |

a list with two components, 'projectors' and 'retrievers'. 'projectors' is a named list of functions with parameters 'x' and 'ncomp', where the intended usage has 'x' inheriting from SingleCellExperiment, and 'ncomp' numeric defining the number of projection components to be retained. 'retrievers' is a named list of functions with parameter 'x', which extracts the ncomp x nsamp projection for each method.

The default sequence is irlba::irlba, umap::umap, Rtsne::Rtsne; see the note on 'warmdim' parameter. Prior to pcmp version 0.3.0, TSNE and UMAP projections were computed 'in one shot' with high target numbers of dimensions. Beginning in 0.3.0, TSNE and UMAP projections are computed targeting 2 and 3 dimensions separately for TSNE, and 2-4 dimensions for UMAP.

1 |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.