boxPlot_feature_twoGroup — boxPlot_feature

This function plots an abundance box plot between two groups for a user-selected feature (lipid).

Usage

boxPlot_feature_twoGroup(
  processed_se,
  feature,
  ref_group,
  test = c("t-test", "Wilcoxon test"),
  transform = c("none", "log10", "square", "cube")
)

Arguments

processed_se: A SummarizedExperiment object constructed by as_summarized_experiment and processed by data_process.
feature: Character. A feature (lipid) for plotting. It must be one of the lipids in the lipid abundance data.
ref_group: Character. Group name of the reference group. It must be one of the group names in the group information table's group column.
test: Character. The method for comparing means. Allowed method include "t-test" and "Wilcoxon test". Default is 't-test'
transform: Character. Method for data transformation. Allowed methods include "none", "log10", "square", and "cube". Select 'none' to skip data transformation. Default is 'log10'.

Value

Return a list of a box plot and a table.

static_boxPlot: abundance box plot of the selected feature.
table_boxplot: table for plotting.
table_stat: statistical table.

Examples

data("de_data_twoGroup")
processed_se <- data_process(
    de_data_twoGroup, exclude_missing=TRUE, exclude_missing_pct=70,
    replace_na_method='min', replace_na_method_ref=0.5,
    normalization='Percentage', transform='log10')
boxPlot_result <- boxPlot_feature_twoGroup(
    processed_se, feature='Cer 38:1;2', ref_group='ctrl', test='t-test',
    transform='log10')