determine_dimensionality: Calculates The Optimum Dimensionality From An Elbow Plot.

In sotaro0214/seuratter: Assists The Current Single Cell RNA Sequencing Analysis Workflow

Description

A function that calculates the optimum dimensionality from an elbow plot. Involves calculating slopes between two consecutive points. The optimum dimensionality will be determined as the point at which slopes no longer change or no visible change occurs to the slopes thereafter. In this function, a dimension is determined optimal when a slope connecting that point to another is flatter than 10 times the flattest slope in the plot and the stdev at that point is proximal to the lower limit. The plot data must be plotted by dims (x-axis) and stdev (y-axis).

Usage

determine_dimensionality(plot_data, cutoff)

Arguments

plot_data	An elbow plot data used for detemining dimensionality, generated by calling ElbowPlot() on a Seurat object.
cutoff	The cutoff that indicates how much data/variance is covered.

Value

Returns an integer that represents the optimal dimensionality that was determined by calculation.

Examples

library(Seurat)
determine_dimensionality(elbow_plot_data, 0.95)

sotaro0214/seuratter documentation built on Dec. 8, 2019, 4:24 p.m.