plot_deSp_twoGroup

Source: R/deSp_twoGroup.R

This function is for plotting the results of lipid species differential expression analysis.

plot_deSp_twoGroup(deSp_se)

Arguments

deSp_se

A SummarizedExperiment object with results computed by deSp_twoGroup.

Value

Return a list of 3 interactive plots, 3 static plots, and 2 tables.

  1. interactive_de_lipid & static_de_lipid: a lollipop chart reveals the lipid species that pass chosen cut-off.

  2. interactive_maPlot & static_maPlot: an MA plot of lipid species.

  3. interactive_volcanoPlot & static_volcanoPlot: a volcano plot of lipid species.

  4. table_de_lipid: table for plotting DE lipid plot.

  5. table_ma_volcano: table for plotting MA plot and volcano plot.

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')
deSp_se <- deSp_twoGroup(processed_se, ref_group='ctrl', test='t-test',
    significant='padj', p_cutoff=0.05, FC_cutoff=1, transform='log10')
deSp_plot <- plot_deSp_twoGroup(deSp_se)
#> Warning: Ignoring unknown aesthetics: text