Count distinct elements for each level of hierarchy per sample

Provides wide, long, and plot views of hierarchy counts.

Value

An R6 class generator.

See also

Other summary: INTERNAL_FUNCTIONS_BY_FAMILY, hierarchy_counts(), summarize_hierarchy()

Public fields

.summary

summarised data frame

.configuration

AnalysisConfiguration object

Methods

Public methods

• HierarchyCountsSample$new()

• HierarchyCountsSample$wide()

• HierarchyCountsSample$long()

• HierarchyCountsSample$plot()

• HierarchyCountsSample$clone()

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HierarchyCountsSample$new()

Create a new HierarchyCountsSample

Usage

HierarchyCountsSample$new(pdata, configuration, nr_children = 1)

Arguments

pdata

data frame

configuration

AnalysisConfiguration

nr_children

minimum number of children to include

---

HierarchyCountsSample$wide()

Return wide-format summary

Usage

HierarchyCountsSample$wide()

---

HierarchyCountsSample$long()

Return long-format summary

Usage

HierarchyCountsSample$long()

---

HierarchyCountsSample$plot()

Return barplot of hierarchy counts

Usage

HierarchyCountsSample$plot()

---

HierarchyCountsSample$clone()

The objects of this class are cloneable with this method.

Usage

HierarchyCountsSample$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

bb <- sim_lfq_data_protein_config()
#> creating sampleName from file_name column
#> completing cases
#> completing cases done
#> setup done
counts <- HierarchyCountsSample$new(bb$data, bb$config)
head(counts$wide())
#> # A tibble: 6 × 3
#> # Groups:   isotopeLabel [1]
#>   isotopeLabel sampleName protein_Id
#>   <chr>        <chr>           <int>
#> 1 light        A_V1                9
#> 2 light        A_V2                9
#> 3 light        A_V3                7
#> 4 light        A_V4               10
#> 5 light        B_V1                9
#> 6 light        B_V2                9