sample_annotation_to_colors {proBatch}R Documentation

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 potting functions

Usage

sample_annotation_to_colors(sample_annotation,
  columns_for_plotting = NULL, sample_id_col = "FullRunName",
  factor_columns = c("MS_batch", "EarTag", "Strain", "Diet", "Sex"),
  not_factor_columns = "DateTime", numeric_columns = "order",
  rare_categories_to_other = TRUE, numeric_palette_type = "brewer",
  granularity = 10)

Arguments

sample_annotation

data matrix with:

  1. sample_id_col (this can be repeated as row names)

  2. biological covariates

  3. technical covariates (batches etc)

columns_for_plotting

only consider these columns from sample_annotation

sample_id_col

name of the column in sample_annotation file, where the filenames (colnames of the data matrix are found)

factor_columns

columns of sample_annotation to be treated as factors. Note that factor and character columns are treated as factors by default.

not_factor_columns

don't treat these columns as factors. This can be used to override the default behaviour of considering factors and character columns as factors.

numeric_columns

columns of sample_annotation to be treated as continuous numeric values.

rare_categories_to_other

if True rare categories will be merged as 'other'

numeric_palette_type

palette to be used for numeric values coloring

granularity

number of colors to map to the number vector (equally spaced between minimum and maximum)

Value

list of colors

Examples

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

[Package proBatch version 1.0.0 Index]