Generate barplots for each feature and perform ANOVA

This function generates bar plots for a specified feature across different groups in the metadata, performing ANOVA and Tukey's HSD test for post-hoc analysis.

Usage

AnovaBarPlot(
  mmo,
  ID_list,
  outdir,
  normalization = "None",
  filter_group = FALSE,
  group_list = NULL,
  save_output = TRUE,
  width = 6,
  height = 6,
  colors = NULL,
  posthoc = NULL
)

Arguments

mmo: The mmo object containing metadata and feature data
ID_list: A list of feature IDs to analyze. Use FeatureToID() to convert feature names to IDs.
outdir: The output directory to save the bar plots and ANOVA results
normalization: The normalization method to use for feature data. Options are 'None', 'Log', 'Meancentered', or 'Z' (default: 'None')
filter_group: A boolean indicating whether to filter the feature values by a specific group list (default: FALSE)
group_list: A list of groups to filter the feature values by, if filter_group is TRUE (default: NULL)
save_output: A logical value indicating whether to save the output plot (default: TRUE)
width: The width of the output plot in inches (default: 6)
height: The height of the output plot in inches (default: 6)
colors: A vector of colors for the groups (default: NULL)
posthoc: A character string indicating the post-hoc test to perform (default: NULL)

Value

A list containing the bar plot and the ANOVA results

Examples

if (FALSE) {
AnovaBarPlot(mmo, ID_list = c("ID_1", "ID_2"), outdir = "output_directory", normalization = 'Z')
AnovaBarPlot(
 mmo, ID_list = c("ID_1", "ID_2"), outdir = "output_directory", normalization = 'Z',
 filter_group = TRUE, group_list = c("Group1", "Group2")
)
}