Introduction
The stimgate package provides tools to identify cells
that have possibly responded to stimulation by comparing unstimulated
and stimulated tubes from the same sample.
Main Functions
The package provides several key functions:
-
stimgate_gate(): Main function to identify cytokine-positive cells by gating -
get_stats(): Generate statistics from gating results -
stimgate_plot(): Visualize identified gates -
stimgate_gate_get(): Extract gate information -
stimgate_fcs_write(): Write FCS files of cytokine-positive cells
Basic Usage
# Basic gating workflow
result <- stimgate_gate(
path_project = "/path/to/project",
.data = gs, # GatingSet object
batch_list = list(batch1 = 1:10, batch2 = 11:20),
marker = list(
list(cut = "IL2", tol = 0.5e-8),
list(cut = "TNFa", tol = 0.5e-8)
)
)
# Get statistics
stats <- get_stats("/path/to/project")
# Get gate table
gates <- get_gate_tbl("/path/to/project")
# Plot gates
plots <- stimgate_plot(
ind = 1:3,
.data = gs,
path_project = "/path/to/project",
marker = c("IL2", "TNFa")
)For more detailed examples and advanced usage, please refer to the function documentation.
sessionInfo()
#> R version 4.5.2 (2025-10-31)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 24.04.3 LTS
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#> tzcode source: system (glibc)
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
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#> other attached packages:
#> [1] stimgate_0.99.1-1
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#> loaded via a namespace (and not attached):
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