defaultProjectors: schematize a sequence of projection methods
In vjcitn/pcmp: projection comparison app
Description
Usage
Arguments
Value
Note
Examples
Description
schematize a sequence of projection methods
Usage
1
defaultProjectors(warmdim = 15)
Arguments
warmdim
numeric(1) defaults to 15 – defines the dimension
reduction using irlba()$u for 'warming up' prior to UMAP or t-SNE runs
Value
a list with two components, 'projectors'
and 'retrievers'. 'projectors' is a named list of
functions with parameters 'x' and 'ncomp',
where the intended usage has 'x' inheriting from SingleCellExperiment,
and 'ncomp' numeric defining the number of projection components
to be retained. 'retrievers' is a named list of functions
with parameter 'x', which extracts the ncomp x nsamp
projection for each method.
Note
The default sequence is irlba::irlba, umap::umap,
Rtsne::Rtsne; see the note on 'warmdim' parameter.
Prior to pcmp version 0.3.0, TSNE and UMAP projections were
computed 'in one shot' with high target numbers of dimensions.
Beginning in 0.3.0, TSNE and UMAP projections are computed
targeting 2 and 3 dimensions separately for TSNE, and 2-4
dimensions for UMAP.
Examples
1
vjcitn/pcmp documentation built on May 25, 2019, 2:21 p.m.
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Description Usage Arguments Value Note Examples
Description
schematize a sequence of projection methods
Usage
1 | defaultProjectors(warmdim = 15)
|
Arguments
warmdim |
numeric(1) defaults to 15 – defines the dimension reduction using irlba()$u for 'warming up' prior to UMAP or t-SNE runs |
Value
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.
Note
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.
Examples
1 |
R Package Documentation
Browse R Packages
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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