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

Description Usage Arguments Details Value Examples

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

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"
)

`.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).

\lifecycle

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 ((dplyr::bind_rows( c('1' = cos(r), '2' = -sin(r)), c('1' = sin(r), '2' = cos(r)) )

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

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

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