Plot variance decomposition — plot

Based on PALMO::variancefeaturePlot() function

Usage

plot_variance(
  var_decomp,
  rank = "Group",
  features = NULL,
  top_n = 20,
  show_ylab = TRUE,
  fontsize = 8
)

Arguments

var_decomp: A data frame output from decomp_variance()
rank: Rank the plot by selected variable (default is "Group")
features: Features to be plotted (default is NULL)
top_n: Top n features ranked by rank to be plotted when features is not specified (default is 20)
show_ylab: Whether to show y axis text (default is TRUE)
fontsize: Font size for the plot (default is 8)

Value

A stacked bar plot showing the percentage of variance explained by each model component (Group, Time, Residual, plus Subject and interaction terms when present). Features are ranked by the specified rank variable (Group or Time) and only the top n features are plotted if features is not specified.

Examples

data(example_obj)
example_obj <- normalise_to_start(example_obj)
#> Normalising to group baseline at each feature's first non-NA time point.

var_decomp <- decomp_variance(example_obj, assay = 1)
#> LMM: exp ~ (1|Group) + (1|Time)  |  Output: Group, Time, Residual
plot_variance(var_decomp, rank = "Time", top_n = 20)
#> Features not specified. Plotting top 20 features ranked by Time.