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

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 class '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 class '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 class '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 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,
  action = "add"
)

# 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,
  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).

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

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())

Examples


counts.MDS =
 tidybulk::se_mini |>
 identify_abundant() |>
 reduce_dimensions( method="MDS", .dims = 3)
#> No group or design set. Assuming all samples belong to one group.
#> Getting the 182 most variable genes
#> tidybulk says: to access the raw results do `attr(..., "internals")$MDS`

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