lipid_profiling

Source: R/lipid_profiling.R

This function provides two plots for users to explore lipid abundance over a specific lipid characteristic.

lipid_profiling(processed_se, char)

Arguments

processed_se

A SummarizedExperiment object constructed by as_summarized_experiment and processed by data_process.

char

Character. A lipid characteristic selected from the common list r eturned by list_lipid_char.

Value

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

  1. interactive_char_barPlot & static_char_barPlot: bar plot classified by selected lipid characteristic. within each group (e.g., PE, PC) of selected characteristics (e.g., class).

  2. interactive_lipid_composition & static_lipid_composition: stacked horizontal bar chart of lipid class composition.

  3. table_char_barPlot: table for plotting char_barPlot.

  4. table_lipid_composition: table for plotting lipid_composition.

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')
list_lipid_char(processed_se)$common_list
#>            Lipid classification            Lipid classification 
#>                      "Category"                    "Main.Class" 
#>            Lipid classification            Lipid classification 
#>                     "Sub.Class"                         "class" 
#>           Fatty acid properties           Fatty acid properties 
#>                            "FA"                          "FA.C" 
#>           Fatty acid properties           Fatty acid properties 
#>     "FA.Chain.Length.Category1"     "FA.Chain.Length.Category2" 
#>           Fatty acid properties           Fatty acid properties 
#>     "FA.Chain.Length.Category3"                         "FA.DB" 
#>           Fatty acid properties           Fatty acid properties 
#>                         "FA.OH"     "FA.Unsaturation.Category1" 
#>           Fatty acid properties           Fatty acid properties 
#>     "FA.Unsaturation.Category2"                       "Total.C" 
#>           Fatty acid properties           Fatty acid properties 
#>                      "Total.DB"                      "Total.FA" 
#>           Fatty acid properties Physical or chemical properties 
#>                      "Total.OH"             "Bilayer.Thickness" 
#> Physical or chemical properties Physical or chemical properties 
#>                     "Bond.type"              "Headgroup.Charge" 
#> Physical or chemical properties Physical or chemical properties 
#>           "Intrinsic.Curvature"             "Lateral.Diffusion" 
#> Physical or chemical properties              Cellular component 
#>        "Transition.Temperature"            "Cellular.Component" 
#>                        Function 
#>                      "Function" 
result <- lipid_profiling(processed_se, char="class")