rotate_dimensions-methods: Rotate two dimensions (e.g., principal components) of an...
In stemangiola/ttBulk: Brings transcriptomics to the tidyverse

rotate_dimensions

R Documentation

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

Description

rotate_dimensions() takes as input 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' (with at least three columns for sample, feature and transcript abundance) or 'SummarizedExperiment' (more convenient if abstracted to tibble with library(tidySummarizedExperiment))
`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

'r lifecycle::badge("maturing")'

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

Underlying custom method: rotation = function(m, d) // r = the angle // m data matrix r = d * pi / 180 ((bind_rows( c('1' = cos(r), '2' = -sin(r)), c('1' = sin(r), '2' = cos(r)) ) |> as_matrix())

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 'SummarizedExperiment' object

Examples


counts.MDS =
 tidybulk::se_mini |>
 identify_abundant() |>
 reduce_dimensions( method="MDS", .dims = 3)

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

stemangiola/ttBulk documentation built on Dec. 14, 2024, 6:12 a.m.