contrast_colors_by_group: Define contrast colors by group colors

In jmw86069/jamses: Jam SummarizedExperiment Stats

Define contrast colors by group colors

Description

Define contrast colors by group colors

Usage

contrast_colors_by_group(
  sedesign,
  sample_color_list = NULL,
  group_name = "Group",
  contrast_sep = "-",
  C_min = 80,
  C_max = 100,
  L_min = 35,
  L_max = 70,
  default_color_style = c("categorical", "navy"),
  verbose = FALSE,
  ...
)

Arguments

sedesign	SEDesign object
sample_color_list	list of colors, with one list element with name defined by group_name, default "Group", so the colors use sample_color_list[[group_name]]. This element should be a character vector of colors, whose names are group names used in the contrast_names(sedesign). The sample_color_list is produced by platjam::design2colors(). Alternatively, a character vector of colors, named by contrast.
group_name	character string for the element in sample_color_list that contains group colors.
contrast_sep	character string used as delimiter between group names in each contrast name, default is "-".
C_min, C_max	numeric value to impose a minimum and maximum chroma (C) value for the resulting contrast color.
L_min, L_max	numeric value to impose a minimum and maximum luminance (C) value for the resulting contrast color.
default_color_style	character string indicating how to assign colors to groups without a color assignment. "categorical": calls colorjam::group2colors() which calls colorjam::rainbowJam() for rainbow categorical colors. any single R color: this one R color is applied to all other groups. any non-R color: assumed to be the name of a color gradient or set, and is resolved by calling jamba::getColorRamp(). It recognizes RColorBrewer and viridis color sets for example. vector of multiple colors: also resolved by calling jamba::getColorRamp() which creates a gradient across the colors.
verbose	logical indicating whether to print verbose output.
...	additional arguments are passed to colorjam::group2colors(), or jamba::getColorRamp() as needed.

Details

This function takes colors assigned to groups, and applies them to contrasts based upon the groups represented in each contrast. Group colors are blended into one output color per contrast, then the color is adjusted for minimum chroma (C) and maximum luminance (L) to ensure the colors have acceptable vibrance.

When sample_color_list is supplied, which defines colors per group, these colors are used as appropriate.

When sample_color_list is not supplied, categorical colors are defined for all observed group names using colorjam::group2colors().

Value

character vector of R colors, with names defined by contrast_names(sedesign).

See Also

Other jam experiment design: check_sedesign(), contrasts_to_factors(), filter_contrast_names(), groups_to_sedesign(), plot_sedesign(), sedesign_to_factors()

jmw86069/jamses documentation built on May 31, 2024, 1:36 p.m.