knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.path = "man/figures/README-", out.width = "100%" )
The goal of faustutils is to provide convenient functions to interrogate a FAUST clustering and extract output from it.
You can install the package from GitHub with:
# install.packages("devtools") devtools::install_github("MiguelRodo/faustutils")
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')
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)
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)
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