geo_sketch: Create downsampled representation of the data with Geometric...

In vitkl/ParetoTI: R toolbox for Archetypal Analysis and Pareto Task Inference on single cell data

Description

geo_sketch() Create a downsampled representation of the data while preserving the structure and rare populations with Geometric Sketch method (https://github.com/brianhie/geosketch, https://www.biorxiv.org/content/10.1101/536730v1). This method splits gene expression space into hypercubes (covering boxes) of equal volume and samples uniformly from those cubes. This reduces the density of the data and cell numbers while preserving global structure. Useful for fitting polytopes to large datasets. First step - find PCs using Facebook PCA method, second step - define hypercubes and sample cells.

Usage

geo_sketch(data, N, assay_slot = "logcounts", use_PCs = TRUE,
  PCs = 100, k = "auto", seed = 4563, replace = FALSE,
  alpha = 0.1, max_iter = 200, verbose = 0, check_installed = TRUE)

Arguments

data	matrix, sparse matrix or SingleCellExperiment (SummarizedExperiment): dim(dimensions * examples)
N	number of cells to sample
assay_slot	slot in data (SingleCellExperiment, SummarizedExperiment) containing matrix to use for PCA and geometric sampling
use_PCs	logical, use PCs (TRUE) or data directly (FALSE)?
PCs	number of PCs to use. Identified using Facebook implementation of PCA (fbpca).
k	Number of covering boxes. When ''auto'‘ and replace is 'True', draws sqrt(X.shape[0]) covering boxes. When '’auto'' and replace is 'False', draws N covering boxes.
seed	Random number generation seed passed to numpy
alpha	Binary search halts when it obtains between 'k * (1 - alpha)' and 'k * (1 + alpha)' covering boxes.
max_iter	Maximum iterations at which to terminate binary seach in rare case of non-monotonicity of covering boxes with box side length.
verbose	report progress

Value

geo_sketch() integer vector of cell indices

vitkl/ParetoTI documentation built on Feb. 11, 2020, 1:36 a.m.