scattergl: Scatter Plot data file

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

Scatter 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 'seriesX' and 'seriesY' contain the raw data for the scatter plot. Column 'group' and 'panel' specify the group the series data belongs to. Optionally, columns 'smoothedMeanX', 'smoothedMeanY' and 'smoothedMeanSE' specify the x, y and standard error respectively of the smoothed conditional mean for the group. Columns 'densityX' and 'densityY' contain the calculated kernel density estimates. Column 'seriesGradientColorscale' contains values to be used with a gradient colorscale when plotting.

Usage

scattergl(
  data,
  variables,
  value = c("smoothedMean", "smoothedMeanWithRaw", "bestFitLineWithRaw", "density",
    "raw"),
  overlayValues = NULL,
  correlationMethod = c("none", "pearson", "sparcc", "spearman"),
  sampleSizes = c(TRUE, FALSE),
  completeCases = c(TRUE, FALSE),
  evilMode = c("noVariables", "allVariables", "strataVariables"),
  idColumn = NULL,
  returnPointIds = c(FALSE, TRUE),
  verbose = c(TRUE, FALSE)
)

Arguments

data	data.frame to make plot-ready data for
variables	veupathUtil::VariableMetadataList and its position in the plot. Recognized plotRef values are 'xAxisVariable', 'yAxisVariable', 'overlayVariable', 'facetVariable1' and 'facetVariable2'
value	character indicating whether to calculate 'smoothedMean', 'bestFitLineWithRaw' or 'density' estimates (no raw data returned), alternatively 'smoothedMeanWithRaw' to include raw data with smoothed mean. Note only 'raw' is compatible with a continuous overlay variable.
overlayValues	veupathUtils::BinList providing overlay values of interest
correlationMethod	character indicating which correlation method to use. One of 'pearson', 'spearman','sparcc' or 'none'. Default is 'none'.
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')
idColumn	character indicating the column name of the id variable in data
returnPointIds	boolean indicating if any point ids should be returned with the scatterplot data.
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' = rnorm(100),
                 'entity.yvar' = rnorm(100),
                 'entity.overlay' = sample(c('red','green','blue'), 100, replace=T), stringsAsFactors = F)

# 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 = 'NUMBER'),
    dataShape = veupathUtils::DataShape(value = 'CONTINUOUS')
  ),
  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
scattergl(df, map, value = 'bestFitLineWithRaw')

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