testClustering: To check one iteration of clustering before running full...

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

Description

This function generates a single clustering iteration of CONCLUS to check whether chosen parameters for dbscan are suitable for your data.

Usage

testClustering(sceObject, dataDirectory, experimentName,
  dbscanEpsilon = 1.4, minPts = 5, perplexities = c(30),
  PCs = c(4), randomSeed = 42, width = 7, height = 7, ...)

Arguments

sceObject	a SingleCellExperiment object with your experiment.
dataDirectory	output directory (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).
dbscanEpsilon	a parameter of fpc::dbscan() function.
minPts	a parameter of fpc::dbscan() function.
perplexities	vector of perplexities (t-SNE parameter).
PCs	a vector of PCs for plotting.
randomSeed	random seed for reproducibility.
width	plot width.
height	plot height.
...	other pdf() arguments.

Value

t-SNE results, a distance graph plot, a t-SNE plot colored by test clustering solution.

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