hippo_dimension_reduction {HIPPO}R Documentation

compute t-SNE or umap of each round of HIPPO

Description

compute t-SNE or umap of each round of HIPPO

Usage

hippo_dimension_reduction(
  sce,
  method = c("umap", "tsne"),
  perplexity = 30,
  featurelevel = 1
)

Arguments

sce

SingleCellExperiment object with hippo object in it.

method

a string that determines the method for dimension reduction: either 'umap' or 'tsne

perplexity

numeric perplexity parameter for Rtsne function

featurelevel

the round of clustering that you will extract features to reduce the dimension

Value

a data frame of dimension reduction result for each k in 1, ..., K

Examples

data(toydata)
set.seed(20200321)
set.seed(20200321)
toydata = hippo(toydata,K = 10,z_threshold = 1,outlier_proportion = 0.01)
toydata = hippo_dimension_reduction(toydata, method="tsne")
hippo_tsne_plot(toydata)

[Package HIPPO version 1.4.0 Index]