heatmap: Heatmap data file

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

Heatmap data file

Description

This function returns the name of a json file containing plot-ready data with one row per group (per panel). Column 'table' contains a nested data.table of z-values for plotting. This table has a column for each x-axis entry and a row for each y-axis entry. Columns 'group' and 'panel' specify the group the series data belongs to. There are two ways to calculate z-values for the heatmap.
1) 'collection' of numeric variables vs single categorical
2) single numeric vs single categorical on a 'series' of dates where yAxisVariable = categorical, xAxisVariable = date and zaxis = numeric

Usage

heatmap(
  data,
  variables,
  value = c("series", "collection"),
  sampleSizes = c(TRUE, FALSE),
  completeCases = c(TRUE, FALSE),
  evilMode = c("noVariables", "allVariables", "strataVariables")
)

Arguments

data	data.frame to make plot-ready data for
variables	veupathUtils VariableMetadataList
value	String indicating which of the three methods to use to calculate z-values ('collection', 'series')
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

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