PropModality {MARVEL}

Tabulate modality proportion

Description

Tabulates and plots the proportion of each modality. This is a wrapper function for PropModality.Doughnut and PropModality.Bar functions.

Usage

PropModality(
  MarvelObject,
  modality.column,
  modality.type,
  event.type,
  across.event.type,
  prop.test = NULL,
  prop.adj = NULL,
  xlabels.size = 8,
  zoom = FALSE,
  yinterval = NULL
)

Arguments

MarvelObject

Marvel object. S3 object generated from AssignModality function.

modality.column

Character string. Can take the value "modality", "modality.var" or "modality.bimodal.adj". Please refer to AssignModality function help page for more details.

modality.type

Character string. basic indicates that only the main modalities (included, excluded, bimodal, middle, multimodal) are analysed. Sub-modalities (primary and dispersed) will be merged. complete indicates that both main and sub-modalities are analysed. Sub-modalities will not be merged.

event.type

Character string. To indicate which event type to analyse. Can take the value "SE", "MXE", "RI", "A5SS" or "A3SS". Specify "all" to include all event types.

across.event.type

Logical. If set to TRUE, the proportion of modality will be compared across the specified event types

prop.test

Character string. Only applicable when across.event.type set to TRUE. chisq Chi-squared test used to compare the proportion of modalities across the different event splicing type. fisher Fisher test used to compare the proportion of modalities across the different splicing event type.

prop.adj

Character string. Only applicable when across.event.type set to TRUE. Adjust p-values generated from prop.test for multiple testing. Options available as per p.adjust function.

xlabels.size

Numeric value. Only applicable when across.event.type set to TRUE. Size of x-axis labels as per ggplot2 function. Default is 8.

zoom

Logical value. Only applicable if across.event.type set to TRUE. If set to TRUE, users can specify the range of the y-axis using yinterval argument. Useful when scrutinasing low-frequency event types, e.g. middle and multimodal.

yinterval

Logical value. Only applicable if across.event.type set to TRUE and zoom set to TRUE.

Value

An object of class S3 containing with new slot $Modality$Prop$DoughnutChart or $Modality$Prop$BarChart.

Examples

marvel.demo <- readRDS(system.file("extdata/data", "marvel.demo.rds", package="MARVEL"))

marvel.demo <- PropModality(MarvelObject=marvel.demo,
                            modality.column="modality.bimodal.adj",
                            modality.type="extended",
                            event.type=c("SE", "MXE", "RI", "A5SS", "A3SS", "AFE", "ALE"),
                            across.event.type=FALSE
                            )

# Check outputs
marvel.demo$Modality$Prop$DoughnutChart$Table
marvel.demo$Modality$Prop$DoughnutChart$Plot