PLS-DA plot with feature loadings

Usage

PLSDAplot(
  mmo,
  color,
  topk = 10,
  outdir,
  normalization = "Z",
  filter_feature = FALSE,
  feature_list = NULL,
  filter_group = FALSE,
  group_list = NULL
)

Arguments

mmo: The mmo object with feature data and metadata
color: A vector of colors for the groups in the plot. Make sure the names correspond to the group names in metadata
topk: The number of top features to display in the plot (default: 10)
outdir: The output file path for the PLS-DA plot
normalization: The normalization method to use for feature data. Options are 'None', 'Log', 'Meancentered', or 'Z' (default: 'Z')
filter_feature: Boolean to filter features by feature_list (default: FALSE)
feature_list: A vector of feature names to filter (default: NULL)
filter_group: Boolean to filter groups by group_list (default: FALSE)
group_list: A vector of group names to filter (default: NULL)

Examples

if (FALSE) {
PLSDAplot(
 mmo, color = c("Control" = "blue", "Treatment1" = "red", "Treatment2" = "green"), 
 topk = 10, outdir = 'PLSDA_plot.pdf', normalization = 'Z', 
 filter_feature = FALSE, filter_group = FALSE
)
PLSDAplot(
 mmo, color = c("Control" = "blue", "Treatment1" = "red"), 
 topk = 5, outdir = 'PLSDA_plot.pdf', normalization = 'Log', 
 filter_feature = TRUE, feature_list = Glucosinolates, 
 filter_group = TRUE, group_list = c("Control", "Treatment1")
)
}