beeswarm: Beeswarm Plot data file

In VEuPathDB/plot.data: Create `data.table`s of Ready to Plot Data

Beeswarm Plot data file

Description

This function returns the name of a json file containing plot-ready data with one row per group (per panel). Columns 'label' and 'jitteredValues' represent the x axis tick label and a random offset (one per y value), repsectively. The 'rawData' column lists the y values to be plotted above each x axis tick. Columns 'group' and 'panel' specify the group the data belong to.

Usage

beeswarm(
  data,
  variables,
  jitter = NULL,
  median = c(FALSE, TRUE),
  overlayValues = NULL,
  sampleSizes = c(TRUE, FALSE),
  completeCases = c(TRUE, FALSE),
  evilMode = c("noVariables", "allVariables", "strataVariables"),
  verbose = c(TRUE, FALSE)
)

Arguments

data	data.frame to make plot-ready data for
variables	veupathUtils VariableMetadataList
jitter	numeric indicating the maximum width by which to randomly offset points.
median	boolean indicating whether to return median value per group (per panel)
overlayValues	veupathUtils::BinList providing overlay values of interest
sampleSizes	boolean indicating if sample sizes should be computed
completeCases	boolean indicating if complete cases should be computed
evilMode	String indicating how evil this plot is ('strataVariables', 'allVariables', 'noVariables')
verbose	boolean indicating if timed logging is desired

Value

character name of json file containing plot-ready data

Evil Mode

An 'evilMode' exists. It will do the following:
- when ‘strataVariables' it will return ’no data' as a regular value for strata vars but will discard such cases for the axes vars.
- when ‘allVariables' it will return ’no data' as a regular value for all variables.
- when 'noVariables' it will do the sensible thing and return complete cases only.
- not return statsTables
- allow smoothed means and agg values etc over axes values where we have no data for the strata vars
- return a total count of plotted incomplete cases
- represent missingness poorly, conflate the stories of completeness and missingness, mislead you and steal your soul

Examples

# Construct example data
df <- data.table('entity.xvar' = sample(c('a','b','c'), 100, replace=T),
                 'entity.yvar' = rnorm(100),
                 'entity.overlay' = sample(c('red','green','blue'), 100, replace=T))

# Create VariableMetadataList that specifies variable role in the plot and supplies variable metadata
variables <- veupathUtils::VariableMetadataList(
  veupathUtils::VariableMetadata(
    variableClass = veupathUtils::VariableClass(value = 'native'),
    variableSpec = veupathUtils::VariableSpec(variableId = 'xvar', entityId = 'entity'),
    plotReference = veupathUtils::PlotReference(value = 'xAxis'),
    dataType = veupathUtils::DataType(value = 'STRING'),
    dataShape = veupathUtils::DataShape(value = 'CATEGORICAL')
  ),
  veupathUtils::VariableMetadata(
    variableClass = veupathUtils::VariableClass(value = 'native'),
    variableSpec = veupathUtils::VariableSpec(variableId = 'overlay', entityId = 'entity'),
    plotReference = veupathUtils::PlotReference(value = 'overlay'),
    dataType = veupathUtils::DataType(value = 'STRING'),
    dataShape = veupathUtils::DataShape(value = 'CATEGORICAL')
  ),
  veupathUtils::VariableMetadata(
    variableClass = veupathUtils::VariableClass(value = 'native'),
    variableSpec = veupathUtils::VariableSpec(variableId = 'yvar', entityId = 'entity'),
    plotReference = veupathUtils::PlotReference(value = 'yAxis'),
    dataType = veupathUtils::DataType(value = 'NUMBER'),
    dataShape = veupathUtils::DataShape(value = 'CONTINUOUS')
  )
)

# Returns the name of a json file
beeswarm(df,map,jitter=0.3)

VEuPathDB/plot.data documentation built on Feb. 20, 2025, 6:33 p.m.