run.phenograph: run.phenograph - Run phenograph clustering

In ImmuneDynamics/Spectre: High-dimensional cytometry and imaging analysis

run.phenograph - Run phenograph clustering

Description

This function allows you to perform phenograph clustering on a data.table

Usage

run.phenograph()

Arguments

ref.dat

NO DEFAULT. A data.table consisting of the 'refernece' data you will use to train the alignment algorithm

Value

Returns a data.table with clustering results added

Author(s)

Thomas M Ashhurst, [e-mail]

References

Ashhurst, T. M., et al. (2019). https://www.ncbi.nlm.nih.gov/pubmed/31077106

Examples

## Not run: 
cell.dat <- Spectre::demo.clustered
cell.dat <- Spectre::do.subsample(cell.dat, 5000)

use.cols <- c("NK11_asinh", "CD3_asinh", "CD45_asinh", 
"Ly6G_asinh", "CD11b_asinh", "B220_asinh", "CD8a_asinh", 
"Ly6C_asinh", "CD4_asinh")

cell.dat <- run.phenograph(dat = cell.dat, use.cols = use.cols)

## End(Not run)

ImmuneDynamics/Spectre documentation built on Oct. 12, 2024, 7:55 p.m.