boxPlot_feature_twoGroup

Source: R/boxPlot_feature_twoGroup.R

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

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.

  1. static_boxPlot: abundance box plot of the selected feature.

  2. table_boxplot: table for plotting.

  3. 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')
boxPlot_result <- boxPlot_feature_twoGroup(
    processed_se, feature='Cer 38:1;2', ref_group='ctrl', test='t-test',
    transform='log10')