factorize_id_column: Convert ID column to a factor with a suitable ordering

In PhotoGEA: Photosynthetic Gas Exchange Analysis

Convert ID column to a factor with a suitable ordering

Description

Converts an ID column to a factor with a suitable ordering. In particular, this function will ensure that any IDs beginning with WT (or any other control group name, case-insensitive) will be ordered before other values. This is helpful when plotting results according to genotype.

Usage

  factorize_id_column(x, ...)

  ## S3 method for class 'character'
factorize_id_column(x, control_group_name = 'WT', ...)

  ## S3 method for class 'data.frame'
factorize_id_column(x, id_column_name, control_group_name = 'WT', ...)

  ## S3 method for class 'exdf'
factorize_id_column(x, id_column_name, control_group_name = 'WT', ...)

Arguments

x	Object to be ordered.
id_column_name	When x is a data.frame or exdf, this argument specifies the column within the table that should be ordered.
control_group_name	A string specifying the name of the control group, such as 'WT' or 'control'.
...	Additional arguments (currently unused).

Details

To choose an ordering, each unique identifier is split into three components: an initial control_group_name (if present), a final numeric value, and any other content in between these two. Then, the identifiers are sorted according to these three values, in order of control_group_name -> other content -> numeric value. Note that capitalization of any initial control_group_name values will be standardized to match the user-specified version.

This system works well with identifiers that represent genotypes/events, or that combine genotype/event with a replicate number.

Value

factorize_id_column.character returns the character vector as a factor with an appropriate ordering.

factorize_id_column.data.frame and factorize_id_column.exdf return a copy of the original table, where one column (specified by id_column_name) has been converted to a factor with an appropriate ordering.

See Also

exdf

Examples

# Identifiers that represent genotypes
genotype_ids <- c('4', 'control', '2', 'CONTROL', '8')

factorize_id_column(genotype_ids, control_group_name = 'control')

# Identifiers that represent `genotype - replicate` values
replicate_ids <- c('4 - 4', 'wT - 2', 'a - 2', 'WT - 1', '4 - 8', 'wt - 9')

factorize_id_column(replicate_ids)

# Data frame
dat <- data.frame(replicate_id = replicate_ids, val = seq_along(replicate_ids))

# Display data in bar chart - note the order of the replicates
lattice::barchart(val ~ replicate_id, data = dat)

# Display factorized data in bar chart - note the order of the replicates
lattice::barchart(val ~ replicate_id, data = factorize_id_column(dat, 'replicate_id'))

# Extended data frame
exdf_obj <- exdf(dat, units = data.frame(replicate_id = '', val = 'm / s'))

exdf_obj <- factorize_id_column(exdf_obj, 'replicate_id')

exdf_obj[, 'replicate_id']

PhotoGEA documentation built on April 11, 2025, 5:48 p.m.