getDimRed: Obtain dimensional reduction data

In kueckelj/celltracer: An Analysis-Toolbox for High-Throughput Cell Imaging Data

Description

Obtain dimensional reduction data

Usage

getDimRed(
  object,
  dim_red_method = "umap",
  with_meta = TRUE,
  with_stats = TRUE,
  phase = "first_tmt"
)

Arguments

object	A valid cell tracer object.
dim_red_method	Character value. The dimensional reduction method.
with_meta	Logical. If set to TRUE the discrete variables of the meta data slot are added to the output data.frame.
with_stats	Logical. If set to TRUE the numeric variables of the stat data slots are added tot he output data.frame.
phase	Character value. Refers to the phase of the experiment. Valid inputs are: 'before_tmt' Uses the data that refers to the time before the treatment. 'first_tmt' Uses the data that refers tot the time after the treatment. Note: This argument is ignored if the experiment set up did not include any treatment or the treatment started right from the beginning.

Value

The data.frame of interest.

kueckelj/celltracer documentation built on June 2, 2021, 6:37 a.m.