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Plot -log10(p-values) of the results obtained after multiple group independence testing

Source: R/groups.R
plotGroupIndependence.Rd

Plot -log10(p-values) of the results obtained after multiple group independence testing

Usage

plotGroupIndependence(
  groups,
  top = 50,
  textSize = 10,
  colourLow = "lightgrey",
  colourMid = "blue",
  colourHigh = "orange",
  colourMidpoint = 150
)

Arguments

groups

multiGroupIndependenceTest object (obtained after running testGroupIndependence())

top

Integer: number of attributes to render

textSize

Integer: size of the text

colourLow

Character: name or HEX code of colour for lower values

colourMid

Character: name or HEX code of colour for middle values

colourHigh

Character: name or HEX code of colour for higher values

colourMidpoint

Numeric: midpoint to identify middle values

Value

ggplot object

See also

parseCategoricalGroups() and testGroupIndependence()

Other functions for data grouping: createGroupByAttribute(), getGeneList(), getSampleFromSubject(), getSubjectFromSample(), groupPerElem(), testGroupIndependence()

Examples

elements <- paste("subjects", 1:50)
ref      <- elements[10:50]
groups   <- list(race=list(asian=elements[1:3],
                           white=elements[4:7],
                           black=elements[8:10]),
                 region=list(european=elements[c(4, 5, 9)],
                             african=elements[c(6:8, 10:50)]))
groupTesting <- testGroupIndependence(ref, groups, elements)
plotGroupIndependence(groupTesting)
#> Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
#> ℹ Please use tidy evaluation idioms with `aes()`.
#> ℹ See also `vignette("ggplot2-in-packages")` for more information.
#> ℹ The deprecated feature was likely used in the psichomics package.
#>   Please report the issue at
#>   <https://github.com/nuno-agostinho/psichomics/issues>.
#> Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
#> ℹ Please use `linewidth` instead.
#> ℹ The deprecated feature was likely used in the psichomics package.
#>   Please report the issue at
#>   <https://github.com/nuno-agostinho/psichomics/issues>.