generateTSNECoordinates: Generate and save t-SNE coordinates with selected parameters.

In PolinaPavlovich/CONCLUS: ScRNA-seq workflow CONCLUS - from CONsensus CLUSters to a meaningful CONCLUSion.

Description

The function generates several t-SNE coordinates based on given perplexity and ranges of PCs. Final number of t-SNE plots is length(PCs)*length(perplexities) It writes coordinates in "dataDirectory/tsnes" subfolder.

Usage

generateTSNECoordinates(sceObject, dataDirectory, experimentName,
  randomSeed = 42, cores = 14, PCs = c(4, 6, 8, 10, 20, 40, 50),
  perplexities = c(30, 40))

Arguments

sceObject	a SingleCellExperiment object with your experiment.
dataDirectory	output directory for CONCLUS (supposed to be the same for one experiment during the workflow).
experimentName	name of the experiment which will appear in filenames (supposed to be the same for one experiment during the workflow).
randomSeed	random seed for reproducibility.
cores	maximum number of jobs that CONCLUS can run in parallel.
PCs	a vector of first principal components. For example, to take ranges 1:5 and 1:10 write c(5, 10).
perplexities	a vector of perplexity (t-SNE parameter).

Value

An object with t-SNE results (coordinates for each plot).

PolinaPavlovich/CONCLUS documentation built on May 10, 2019, 2:42 p.m.