boxPlot_feature_multiGroup — boxPlot_feature

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

Usage

boxPlot_feature_multiGroup(
  processed_se,
  feature,
  ref_group,
  test = c("One-way ANOVA", "Kruskal–Wallis test"),
  post_hoc_sig = c("pval", "padj"),
  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 "One-way ANOVA" and "Kruskal–Wallis test". Default is 'One-way ANOVA'.
post_hoc_sig: Character. The p-value to be used for to determine significance, which is only applicable for the post hoc test after the Kruskal-Wallis test. Must be one of "padj" (adjusted p-value) or "pval" (p-value). Default is 'pval'. ##One-way ANOVA只能是padj, Kruskal-Wallis test可以是pval or padj
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("se_multiGroup")
processed_se <- data_process(
    se=se_multiGroup, 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_multiGroup(
    processed_se, feature='PE O- 17:0;0_20:3;0', ref_group='ctrl',
    test='One-way ANOVA', post_hoc_sig='padj', transform='log10')