FLOWMAP: FLOWMAP - generate FLOWMAPR analysis results from FCS files...

In zunderlab/FLOWMAP: Graph-based visualizations of high-dimensional single-cell data across time

FLOWMAP - generate FLOWMAPR analysis results from FCS files in R

Description

FLOWMAP generates FLOWMAPR analysis results from FCS files. For more information, as well as a guide for how to choose the best settings for your analysis, go to our GitHub repo https://github.com/zunderlab/FLOWMAP/.

Usage

FLOWMAP(
  mode = c("single", "multi", "one", "static-multi"),
  files,
  var.remove = c(),
  var.annotate = NULL,
  clustering.var,
  cluster.numbers = 100,
  cluster.mode = "hclust",
  distance.metric = "manhattan",
  minimum = 2,
  maximum = 5,
  save.folder = getwd(),
  subsamples = 200,
  name.sort = TRUE,
  out_folder_basename = NA,
  downsample = FALSE,
  seed.X = 1,
  savePDFs = TRUE,
  graph.out = c("ForceDirected"),
  which.palette = "bluered",
  exclude.pctile = NULL,
  target.pctile = NULL,
  target.number = NULL,
  target.percent = NULL,
  k = 10,
  umap.n.neighbors = 10,
  umap.n.components = 2,
  ...
)

Arguments

mode	FLOWMAPR mode to use in analysis based on starting input, available options include c("single", "multi", "one", "static-multi")
files	File paths for FCS files to be used or a folder containing the FCS files to be used in analysis
var.remove	Vector naming channels to be removed from all downstream analysis, default value is an empty vector, meaning that no channels will be removed
var.annotate	List mapping channel names to user-specified names to properly annotate all FCS file data, default value is NULL, which will then autogenerate the var.annotate values using the ConstructVarAnnotate() function
clustering.var	Vector naming channels to be used to calculate distances/differences between cells for clustering (if requested) and edge-drawing steps
cluster.numbers	A single numeric or a vector of numerics specifying how many clusters to generate from each separate FCS file
cluster.mode	Character specifying which clustering algorithm to use, valid options include c("hclust", "kmeans")
distance.metric	Character specifying which metric to use to calculate between-node distances, valid options include c("manhattan", "euclidean")
minimum	Numeric value specifying the minimum number of edges that will be allotted during each density-dependent edge-building step of the FLOW-MAP graph, default value is set to 2, no less than 2 is recommended
maximum	Numeric value specifying the maximum number of edges that will be allotted during each density-dependent edge-building step of the FLOW-MAP graph, default value is set to 5, no less than 3 is recommended
save.folder	Directory where all results generated should be saved
subsamples	A single numeric or a vector of numerics specifying how many cells to subsample from each FCS file
name.sort	Logical specifying whether to sort FCS file path names alphanumerically or use them in the order supplied by the user
out_folder_basename	= NA by default, provide string base name is desired
downsample	Logical specifying whether to use SPADE density-dependent downsampling
seed.X	Numeric value for the seed to set for reproducible FLOWMAPR runs
savePDFs	Logical specifying whether to generate PDFs for the resolved graph with nodes colored by each parameter
graph.out	TBD
which.palette	Optional variable, character specifying which color palette to use in generated PDFs, valid options include c("bluered", "jet", "CB"), where "CB" is a colorblind-friendly option
exclude.pctile	Optional variable, numeric value for the downsampling_exclude_pctile variable used as described in the SPADE driver function, see the documentation for the spade package at https://github.com/nolanlab/spade
target.pctile	Optional variable, numeric value for the downsampling_target_pctile variable used as described in the SPADE driver function, see the documentation for the spade package at https://github.com/nolanlab/spade
target.number	Optional variable, numeric value for the downsampling_target_number variable used as described in the SPADE driver function, see the documentation for the spade package at https://github.com/nolanlab/spade
target.percent	Optional variable, numeric value for the downsampling_target_percent variable used as described in the SPADE driver function, see the documentation for the spade package at https://github.com/nolanlab/spade
umap.n.neighbors	TBD
umap.n.components	TBD

Value

the force-directed layout resolved igraph graph object

zunderlab/FLOWMAP documentation built on Sept. 7, 2024, 6:31 p.m.