sample_annotation_to_colors: Generate colors for sample annotation

In symbioticMe/proBatch: Tools for Diagnostics and Corrections of Batch Effects in Proteomics

Generate colors for sample annotation

Description

Convert the sample annotation data frame to list of colors the list is named as columns included to use in plotting functions

Usage

sample_annotation_to_colors(sample_annotation,
  sample_id_col = "FullRunName", factor_columns = c("MS_batch",
  "EarTag", "digestion_batch", "Strain", "Diet"),
  numeric_columns = c("DateTime", "order"),
  rare_categories_to_other = TRUE, guess_factors = FALSE,
  numeric_palette_type = "brewer")

Arguments

sample_annotation	data frame with: sample_id_col (this can be repeated as row names) biological covariates technical covariates (batches etc) . See help("example_sample_annotation")
sample_id_col	name of the column in sample_annotation table, where the filenames (colnames of the data_matrix are found).
factor_columns	columns of sample_annotation to be treated as factors. Sometimes categorical variables are depicted as integers (e.g. in column "Batch", values are 1, 2 and 3), specification here allows to map them correctly to qualitative palettes.
numeric_columns	columns of sample_annotation to be treated as continuous numeric values.
rare_categories_to_other	if True rare categories will be merged into the value "other"
guess_factors	whether attempt which of the factor_columns are actually numeric
numeric_palette_type	palette to be used for numeric values coloring (can be 'brewer' and 'viridis')

Value

list of three items:

1. list of colors;

2. data frame of colors;

3. new sample annotation (e.g. rare factor levels merged into "other")

Examples

color_scheme <- sample_annotation_to_colors (example_sample_annotation, 
factor_columns = c('MS_batch','EarTag', "Strain", 
"Diet", "digestion_batch", "Sex"),
numeric_columns = c('DateTime', 'order'))

symbioticMe/proBatch documentation built on April 9, 2023, 11:59 a.m.