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

Source: R/rotate_dimensions.R

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
)

# S4 method for class '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
)

# S4 method for class '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
)

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)

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

A `SummarizedExperiment` object

Details

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

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

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

References

Mangiola, S., Molania, R., Dong, R., Doyle, M. A., & Papenfuss, A. T. (2021). tidybulk: an R tidy framework for modular transcriptomic data analysis. Genome Biology, 22(1), 42. doi:10.1186/s13059-020-02233-7

Examples

## Load airway dataset for examples

  data('airway', package = 'airway')
  # Ensure a 'condition' column exists for examples expecting it

    SummarizedExperiment::colData(airway)$condition <- SummarizedExperiment::colData(airway)$dex



counts.MDS =
 airway |>
 identify_abundant() |>
 reduce_dimensions( method="MDS", .dims = 3)
#> Warning: All samples appear to belong to the same group.
#> Getting the 500 most variable genes
#> [1] "MDS result_df colnames: sample, 1, 2, 3"
#> tidybulk says: to access the raw results do `metadata(.)$tidybulk$MDS`

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