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Update community and layer color palettes in MixMashNet objects

Source: R/update_palette.R
update_palette.Rd

Updates the color palettes associated with communities and/or layers in fitted mixMN_fit and multimixMN_fit objects.

For mixMN_fit objects, community_colors must be a named character vector specifying colors for community labels in object$communities$palette.

For multimixMN_fit objects, community_colors must be a named list whose elements correspond to layer names. Each element must be a named character vector specifying colors for the community labels of that layer. The list may be partial, so only the specified layers are updated.

For multimixMN_fit objects, layer_colors updates the palette stored in object$layers$palette.

The function replaces only the colors corresponding to the provided names, leaving all other colors unchanged. Unknown layer names, community labels, or layer labels are ignored with a warning.

Usage

update_palette(object, ...)

# S3 method for class 'mixMN_fit'
update_palette(object, community_colors = NULL, layer_colors = NULL, ...)

# S3 method for class 'multimixMN_fit'
update_palette(object, community_colors = NULL, layer_colors = NULL, ...)

Arguments

object

An object of class mixMN_fit or multimixMN_fit.

...

Further arguments passed to methods.

community_colors

For mixMN_fit objects, an optional named character vector specifying new colors for communities.

For multimixMN_fit objects, an optional named list whose names are layer names and whose elements are named character vectors specifying new colors for communities within each layer.

layer_colors

Optional named character vector specifying new colors for layers. Only applicable to multimixMN_fit objects.

Value

The input object, with updated community and/or layer palettes.

Details

For single layer fits, only community_colors is used.

For multilayer fits:

  • community_colors updates community palettes within the specified layers;

  • layer_colors updates the palette of the layers themselves.

For multilayer fits, community_colors can be partial: layers not included in the list are left unchanged.

Examples

data(bacteremia)

vars <- c("WBC", "NEU", "HGB", "PLT", "CRP")
df <- bacteremia[, vars]

fit <- mixMN(
  data = df,
  lambdaSel = "EBIC",
  reps = 0,
  seed_model = 42,
  compute_loadings = FALSE,
  progress = FALSE
)

fit$communities$palette
#>         1         2 
#> "#E16A86" "#00AD9A" 

fit2 <- update_palette(
  fit,
  community_colors = c("1" = "red", "2" = "blue")
)

fit2$communities$palette
#>      1      2 
#>  "red" "blue" 

set.seed(1)
plot(fit2)