The goal of UtilsFaustSV is to provide convenient functions to interrogate a FAUST clustering and extract output from it.
You can install the package from GitHub with:
if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes")
remotes::install_github("SATVILab/UtilsFaustSV")
This is a basic example which shows you how to solve a common problem:
library(UtilsFaustSV)
First save the directory FAUST saved results to:
# set the FAUST project path
proj_path <- usethis::proj_path('tests/testthat')
#> v Setting active project to 'C:/Users/migue/Work/Packages/UtilsFAUSTSV'
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)