Convert ID column to a factor with a suitable ordering

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).

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.

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.

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')
#> [1] 4       control 2       control 8      
#> Levels: control 2 4 8

# 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)
#> [1] 4 - 4  WT - 2 a - 2  WT - 1 4 - 8  WT - 9
#> Levels: WT - 1 WT - 2 WT - 9 4 - 4 4 - 8 a - 2

# 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']
#> [1] 4 - 4  WT - 2 a - 2  WT - 1 4 - 8  WT - 9
#> Levels: WT - 1 WT - 2 WT - 9 4 - 4 4 - 8 a - 2