Plot tSNE map of the cells and highlight SC3 clusters with colors

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Description

tSNE (t-Distributed Stochastic Neighbor Embedding) method is used to map high-dimensional data to a 2D space while preserving local distances between cells. tSNE has become a very popular visualisation tool. SC3 imports the Rtsne function from the Rtsne package to perform the tSNE analysis. The colors on the plot correspond to the clusters identified by SC3. One of the most sensitive parameters in tSNE analysis is the so-called perplexity. SC3 defines the default perplexity as N/5, where N is the number of cells.

Usage

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sc3_plot_tsne.SCESet(object, k,
  perplexity = floor(ncol(get_processed_dataset(object))/5), seed = 1234567)

## S4 method for signature 'SCESet'
sc3_plot_tsne(object, k,
  perplexity = floor(ncol(get_processed_dataset(object))/5), seed = 1234567)

Arguments

object

an object of 'SCESet' class

k

number of clusters

perplexity

perplexity parameter used in Rtsne for tSNE tranformation

seed

random seed used for tSNE transformation

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