fsom_aof: Prepares FlowSOM
In prybakowska/CytoQP: Cytometry data quality control and cleaninig

fsom_aof

R Documentation

Prepares FlowSOM

Description

Builds FlowSOM object

Usage

fsom_aof(
  fcs_files,
  phenotyping_markers,
  markers_to_score,
  nCells = length(fcs_files) * 10000,
  xdim = 10,
  ydim = 10,
  nClus = 10,
  out_dir = NULL,
  batch = NULL,
  arcsine_transform = TRUE,
  transform_list = NULL,
  my_colors = NULL,
  seed = NULL,
  to_plot = TRUE
)

Arguments

`fcs_files`	Character, full path to fcs_files.
`phenotyping_markers`	Character vector, marker names to be used for clustering, can be full marker name e.g. "CD45" or "CD" if all CD-markers needs to be plotted.
`markers_to_score`	Character vector, marker names to be used for flowsom clustering including DNA marker Iridium and viability staining if available. Can be full marker name e.g. "CD45" or pattern "CD" if all CD-markers needs to be plotted. Default is set to NULL, thus the aof scores will be calculated for the markers included in phenotyping_markers.
`nCells`	Numeric, the total number of cells, to use for FlowSOM clustering. This number is determined by total number of fcs files, as a default 10000 cells is used per file
`xdim`	Numeric, as in FlowSOM, parameter to pass to FlowSOM, width of the SOM grid
`ydim`	Numeric, as in FlowSOM, parameter to pass to FlowSOM, height of the SOM grid
`nClus`	Numeric, exact number of clusters for metaclustering
`out_dir`	Character, pathway to where the FlowSOM clustering plot should be saved, default is set to working directory.
`batch`	Character, the name of the acquisition batch for each fcs file. This name is passed to FlowSOM plot name, default is set to NULL
`arcsine_transform`	Logical, if the data should be transformed with arcsine transformation and cofactor 5. Default set to TRUE.
`transform_list`	Transformation list to pass to the flowCore transform function see flowCore::transformList.
`my_colors`	An array specifying colors to be used for the background coloring of metaclusters in FlowSOM and t-SNE plot. Must have a length equal to the nClus.If NULL (default) colors defined in FlowSOM package will be used.
`seed`	numeric, set to obtain reproducible results, default set to NULL.
`to_plot`	Logical, if FlowSOM tree and t-SNE map should be plotted, default set to TRUE.