reduce_dimensions-methods: Dimension reduction of the feature value data

In stemangiola/nanny: High-Level Data Analysis and Manipulation in 'tidyverse' Style

Dimension reduction of the feature value data

Description

reduce_dimensions() takes as input a 'tbl' formatted as | <element> | <feature> | <value> | <...> | and calculates the reduced dimensional space of the feature value. The functions available are PCA, MDS (Robinson et al., 2010, <doi:10.1093/bioinformatics/btp616>), tSNE (Laurens van der Maaten, 2009)

Usage

reduce_dimensions(
  .data,
  .element,
  .feature,
  .value,
  method,
  .dims = 2,
  top = Inf,
  of_elements = TRUE,
  transform = NULL,
  scale = TRUE,
  action = "add",
  ...
)

## S3 method for class 'spec_tbl_df'
reduce_dimensions(
  .data,
  .element,
  .feature,
  .value,
  method,
  .dims = 2,
  top = Inf,
  of_elements = TRUE,
  transform = NULL,
  scale = TRUE,
  action = "add",
  ...
)

## S3 method for class 'tbl_df'
reduce_dimensions(
  .data,
  .element,
  .feature,
  .value,
  method,
  .dims = 2,
  top = Inf,
  of_elements = TRUE,
  transform = NULL,
  scale = TRUE,
  action = "add",
  ...
)

Arguments

.data	A 'tbl' formatted as | <element> | <feature> | <value> | <...> |
.element	The name of the element column (normally elements).
.feature	The name of the feature column (normally features)
.value	The name of the column including the numerical value the clustering is based on (normally feature value)
method	A character string. The dimension reduction algorithm to use (PCA, MDS, tSNE).
.dims	A list of integer vectors corresponding to principal components of interest (e.g., list(1:2, 3:4, 5:6))
top	An integer. How many top genes to select for dimensionality reduction
of_elements	A boolean. In case the input is a nanny object, it indicates Whether the element column will be element or feature column
transform	A function to use to tranforma the data internalli (e.g., log1p)
scale	A boolean for method="PCA", this will be passed to the 'prcomp' function. It is not included in the ... argument because although the default for 'prcomp' if FALSE, it is advisable to set it as TRUE.
action	A character string. Whether to join the new information to the input tbl (add), or just get the non-redundant tbl with the new information (get).
...	Further parameters passed to the function prcomp if you choose method="PCA" or Rtsne if you choose method="tSNE"

Details

\lifecycle

maturing

This function reduces the dimensions of the feature values. It can use multi-dimensional scaling (MDS) of principal component analysis (PCA).

Value

A tbl object with additional columns for the reduced dimensions

A tbl object with additional columns for the reduced dimensions

A tbl object with additional columns for the reduced dimensions

Examples

  reduce_dimensions(mtcars_tidy, car_model, feature, value, method="PCA")
  
  reduce_dimensions(mtcars_tidy, car_model, feature, value, method="MDS")
  
  reduce_dimensions(mtcars_tidy, car_model, feature, value, method="tSNE")

stemangiola/nanny documentation built on July 29, 2023, 1:23 a.m.