rotate_dimensions {tidybulk} | R Documentation |
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' (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). |
'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 ((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 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
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)