rotate_dimensions {tidybulk}R Documentation

Rotate two dimensions (e.g., principal components) of an arbitrary angle

Description

rotate_dimensions() takes as imput a 'tbl' formatted as | <DIMENSION 1> | <DIMENSION 2> | <...> | and calculates the rotated dimensional space of the transcript abundance.

Usage

rotate_dimensions(
  .data,
  dimension_1_column,
  dimension_2_column,
  rotation_degrees,
  .element = NULL,
  of_samples = TRUE,
  dimension_1_column_rotated = NULL,
  dimension_2_column_rotated = NULL,
  action = "add"
)

## S4 method for signature 'spec_tbl_df'
rotate_dimensions(
  .data,
  dimension_1_column,
  dimension_2_column,
  rotation_degrees,
  .element = NULL,
  of_samples = TRUE,
  dimension_1_column_rotated = NULL,
  dimension_2_column_rotated = NULL,
  action = "add"
)

## S4 method for signature 'tbl_df'
rotate_dimensions(
  .data,
  dimension_1_column,
  dimension_2_column,
  rotation_degrees,
  .element = NULL,
  of_samples = TRUE,
  dimension_1_column_rotated = NULL,
  dimension_2_column_rotated = NULL,
  action = "add"
)

## S4 method for signature 'tidybulk'
rotate_dimensions(
  .data,
  dimension_1_column,
  dimension_2_column,
  rotation_degrees,
  .element = NULL,
  of_samples = TRUE,
  dimension_1_column_rotated = NULL,
  dimension_2_column_rotated = NULL,
  action = "add"
)

## S4 method for signature 'SummarizedExperiment'
rotate_dimensions(
  .data,
  dimension_1_column,
  dimension_2_column,
  rotation_degrees,
  .element = NULL,
  of_samples = TRUE,
  dimension_1_column_rotated = NULL,
  dimension_2_column_rotated = NULL,
  action = "add"
)

## S4 method for signature 'RangedSummarizedExperiment'
rotate_dimensions(
  .data,
  dimension_1_column,
  dimension_2_column,
  rotation_degrees,
  .element = NULL,
  of_samples = TRUE,
  dimension_1_column_rotated = NULL,
  dimension_2_column_rotated = NULL,
  action = "add"
)

Arguments

.data

A 'tbl' formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> |

dimension_1_column

A character string. The column of the dimension 1

dimension_2_column

A character string. The column of the dimension 2

rotation_degrees

A real number between 0 and 360

.element

The name of the element column (normally samples).

of_samples

A boolean. In case the input is a tidybulk object, it indicates Whether the element column will be sample or transcript column

dimension_1_column_rotated

A character string. The column of the rotated dimension 1 (optional)

dimension_2_column_rotated

A character string. The column of the rotated dimension 2 (optional)

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).

Details

Maturing lifecycle

This function to rotate two dimensions such as the reduced dimensions.

Value

A tbl object with additional columns for the reduced dimensions. additional columns for the rotated dimensions. The rotated dimensions will be added to the original data set as '<NAME OF DIMENSION> rotated <ANGLE>' by default, or as specified in the input arguments.

A tbl object with additional columns for the reduced dimensions. additional columns for the rotated dimensions. The rotated dimensions will be added to the original data set as '<NAME OF DIMENSION> rotated <ANGLE>' by default, or as specified in the input arguments.

A tbl object with additional columns for the reduced dimensions. additional columns for the rotated dimensions. The rotated dimensions will be added to the original data set as '<NAME OF DIMENSION> rotated <ANGLE>' by default, or as specified in the input arguments.

A tbl object with additional columns for the reduced dimensions. additional columns for the rotated dimensions. The rotated dimensions will be added to the original data set as '<NAME OF DIMENSION> rotated <ANGLE>' by default, or as specified in the input arguments.

A 'SummarizedExperiment' object

A 'SummarizedExperiment' object

Examples


counts.MDS =  reduce_dimensions(tidybulk::counts_mini, sample, transcript, count, method="MDS", .dims = 3)

counts.MDS.rotated =  rotate_dimensions(counts.MDS, `Dim1`, `Dim2`, rotation_degrees = 45, .element = sample)



[Package tidybulk version 1.0.2 Index]