README.md

In MiguelRodo/faustutils: Additional functions to extract and plot FAUST output

faustutils

The goal of faustutils is to provide convenient functions to interrogate a FAUST clustering and extract output from it.

Installation

You can install the package from GitHub with:

# install.packages("devtools")
devtools::install_github("MiguelRodo/faustutils")

Example

This is a basic example which shows you how to solve a common problem:

library(faustutils)

First save the directory FAUST saved results to:

# set the FAUST project path
proj_path <- usethis::proj_path('tests/testthat')
#> √ Setting active project to 'C:/Users/migue/OneDrive - University of Cape Town/Work/PhD/Code/faustutils'

You can get the names of the markers FAUST used to cluster and the number of levels for each (after FAUST has clustered):

get_faust_markers_and_levels(project_path = proj_path)
#>         CD33          CD7         CCR7      CD8-IgD HLA-DR-beads         CD14 
#>            2            2            2            2            2            2 
#>         CD27          CD4         CD16         CD20   TCRgd-CD19          CD3 
#>            2            2            2            2            2            2 
#>       CD45RA        CXCR5 
#>            2            2

You can save FAUST-identified clusters as FCS files using only a subset of the markers (not run):

save_faust_pop(project_path = proj_path, pop = list("CD3" = 2, "CD4" = 2), 
               gs = gs) # set gs to be the GatingSet FAUST clustered

You can get a table of counts of FAUST-identified clusters defined using only a subset of the markers used (not run):

get_pop_counts(project_path = proj_path, 
               pop = c("CD4" = "-", "CD8" = "+"))

You can save plots of counts of FAUST-identified clusters, where the clusters are defined using only a subset of the markers (not run):

# plot all subsets that match these annotations individually
pop <- c("CD3" = "+", "CD4" = "+", "CD8-IgD" = "-")
plot_faust_count(project_path = proj_path,
                 pop = pop)

# plot total counts of subsets that match these annotations
# within each list element
pop <- list(c("CD3" = "+", "CD4" = "+", "CD8-IgD" = "-"),
           c("CD3" = "+", "CD4" = "-", "CD8-IgD" = "+"))
plot_faust_count(project_path = proj_path,
                 pop = pop)

MiguelRodo/faustutils documentation built on March 26, 2021, 11:50 p.m.