gates: Gates

In CytobankBridgeR: Bridging and Extending the CytobankAPI Package in R to the Cytobank Web Application

Description

Gates High Level Functions

Usage

gates.apply_cluster_gates(UserSession, experiment_id, name, clusters,
  channel_name, integer_min = 1, integer_max = max(clusters),
  grouped = FALSE, timeout = 60)

Arguments

UserSession	Cytobank UserSession object (created via the authenticate function)
experiment_id	integer representing an experiments ID
name	character representing a cluster prefix (if grouped=FALSE) or multicluster gate name
clusters	integer vector representing the clusters to gate - There are 2 modes of operation: 1) grouped=FALSE: clusters represent individual integer clusters to gate, this will create multiple gates that represents multiple individual populations 2) grouped=TRUE: clusters represent a multi-integer cluster to gate, this will create one gate that represents one population around the integer clusters specified
channel_name	character representing the channel short name
integer_min	integer representing the minimum cluster integer for setting scales [optional] - The default is set to 1, this assumes clusters begin at 1, but can be changed if there is any +/- offset - The minimum scale will be set to integer_min-1 (0 by)
integer_max	integer representing the maximum cluster integer for setting scales [optional] - The default is the maximum number presented within the clusters vector, but can be set to any integer - The max scale will be set to integer_max+1
grouped	logical representing whether to gate a vector of integer clusters as individual integer clusters (grouped=FALSE), or together as a single multicluster (grouped=TRUE)
timeout	integer representing the request timeout time in seconds [optional]

Details

gates.apply_cluster_gates Apply cluster gate(s) to specific clusters via an integer vector

Examples

gates.apply_cluster_gates(cyto_session, 22, name="cluster_names",
  clusters=c(1,5,9), channel_name="cluster_id")

CytobankBridgeR documentation built on May 2, 2019, 8:27 a.m.