plot_data_process

This function plots the differences in abundance data before and after data processing.

plot_data_process(se, processed_se)

Arguments

se

A SummarizedExperiment object construct by as_summarized_experiment.

processed_se

A SummarizedExperiment object constructed by as_summarized_experiment and processed by data_process.

Value

Return a list with 4 static plots and 4 interactive plots.

1. static_boxPlot_before: a static bar plot of lipid abundance before data processing.

2. static_densityPlot_before: a static density plot of lipid abundance before data processing.

3. static_boxPlot_after: a static bar plot of lipid abundance before data processing.

4. static_densityPlot_after: a static density plot of lipid abundance after data processing.

5. interactive_boxPlot_before: an interactive bar plot of lipid abundance before data processing.

6. interactive_densityPlot_before: an interactive density plot of lipid abundance before data processing.

7. interactive_boxPlot_after: an interactive bar plot of lipid abundance after data processing.

8. interactive_densityPlot_after: an interactive density plot of lipid abundance after data processing.

Examples

data("profiling_data")
processed_se <- data_process(
    profiling_data, exclude_missing=TRUE, exclude_missing_pct=70,
    replace_na_method='min', replace_na_method_ref=0.5,
    normalization='Percentage')
plots <- plot_data_process(profiling_data, processed_se)
#> Warning: The following aesthetics were dropped during statistical transformation:
#> y_plotlyDomain
#> ℹ This can happen when ggplot fails to infer the correct grouping structure in
#>   the data.
#> ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
#>   variable into a factor?
#> Warning: The following aesthetics were dropped during statistical transformation:
#> y_plotlyDomain
#> ℹ This can happen when ggplot fails to infer the correct grouping structure in
#>   the data.
#> ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
#>   variable into a factor?