run.flowsom: Run the FlowSOM algorithm

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

Run the FlowSOM algorithm

Description

Method to run the FlowSOM clustering algorithm. This function runs FlowSOM on a data.table with cells (rows) vs markers (columns) with new columns for FlowSOM clusters and metaclusters. Output data will be "flowsom.res.original" (for clusters) and "flowsom.res.meta" (for metaclusters). Uses the R packages "FlowSOM" for clustering, "flowCore" for handling .fcs files, "Biobase" for creating a flow frame, "data.table" for handling data.table format.

Usage

run.flowsom(dat, use.cols, meta.k, xdim, ydim, clust.seed, 
meta.seed, clust.name, meta.clust.name)

Arguments

dat	NO DEFAULT. data.frame. Input sample.
use.cols	NO DEFAULT. Vector of column names to use for clustering.
xdim	DEFAULT = 14. Numeric. Number of first level clusters across the x-axis. xdim x ydim = total number of first level FlowSOM clusters.
ydim	DEFAULT = 14. Numeric. Number of first level clusters across the y-axis. xdim x ydim = total number of first level FlowSOM clusters.
meta.k	DEFAULT = 'auto'. If set to 'auto', then number of metaclusters will be determined automatically. Alternatively, can specify the desired number of metaclusters to create. If set to zero (0), no metaclusters will be created.
max.meta	DEFAULT = 20. Only used if meta.k is set to 'auto'. This parameter indicates the maximum number of metaclusters FlowSOM will try out when determining the optimal number of metaclusters for the dataset.
clust.seed	DEFAULT = 42 Numeric. Clustering seed for reproducibility.
meta.seed	DEFAULT = 42 Numeric. Metaclustering seed for reproducibility.
clust.name	DEFAULT = "FlowSOM_cluster". Character. Name of the resulting 'cluster' parameter.
meta.clust.name	DEFAULT = "FlowSOM_metacluster". Character. Name of the resulting 'metacluster' parameter.
mem.ctrl	DEFAULT = TRUE. Runs gc() (garbage collection) after a number of steps to free up memory that hasn't been released quickly enough.

Author(s)

Thomas Ashhurst, [e-mail] Felix Marsh-Wakefield, [e-mail]

Examples

# Run FlowSOM on demonstration dataset
res <- Spectre::run.flowsom(Spectre::demo.clustered,
                            use.cols = c("NK11_asinh", "CD3_asinh", 
                            "CD45_asinh", "Ly6G_asinh", "CD11b_asinh", 
                            "B220_asinh", "CD8a_asinh", "Ly6C_asinh", 
                            "CD4_asinh"))

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