FLOWMAPfromDF: FLOWMAPfromDF - generate FLOWMAPR analysis results from...

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

FLOWMAPfromDF - generate FLOWMAPR analysis results from dataframes in R

Description

FLOWMAP generates FLOWMAPR analysis results from dataframe(s). 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

FLOWMAPfromDF(
  mode = c("single", "multi", "one", "static-multi"),
  df,
  project.name,
  clustering.var,
  distance.metric = "manhattan",
  minimum = 2,
  maximum = 5,
  save.folder = getwd(),
  time.col.label = "Time",
  condition.col.label = NULL,
  name.sort = TRUE,
  clustering = FALSE,
  seed.X = 1,
  graph.out = c("ForceDirected"),
  savePDFs = TRUE,
  which.palette = "bluered",
  cluster.numbers = NULL,
  cluster.mode,
  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")
df	single dataframe, list of dataframes with each member belonging to single-cell data from a different timepoint, or a list of lists of dataframes belonging to the same timepoint, but coming from different conditions, to be used in analysis
project.name	Character string to label file output of FLOWMAPR analysis
clustering.var	Vector naming channels to be used to calculate distances/differences between cells for clustering (if requested) and edge-drawing steps
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
time.col.label	Character specifying the name of the channel with the time labels for each cell
condition.col.label	Character specifying the name of the channel with the condition labels for each cell
name.sort	Logical specifying whether to sort FCS file path names alphanumerically or use them in the order supplied by the user
clustering	Logical specifying whether to cluster single-cell data
seed.X	Numeric value for the seed to set for reproducible FLOWMAPR runs
graph.out	TBD
savePDFs	Logical specifying whether to generate PDFs for the resolved graph with nodes colored by each parameter
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
cluster.numbers	Optional variable, single numeric or a vector of numerics specifying how many clusters to generate from each separate dataframe
cluster.mode	Character specifying which clustering algorithm to use, valid options include c("hclust", "kmeans")
k
umap.n.neighbors	TBD
umap.n.components	TBD
out_folder_basename	= NA by default, provide string base name is desired

Value

the force-directed layout resolved igraph graph object

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