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Plot Z-score group differences with statistical significance

Source: R/CreateZScorePlot.R
PlotZScore.Rd

This function generates a Z-score plot to compare multiple variables across different groups. It offers options for parametric or non-parametric tests, ordinal treatment, and custom labeling. Significant p-values and FDR-adjusted p-values are highlighted on the plot.

CreateZScorePlot() has been superseded by PlotZScore(). It remains available as a backwards-compatible alias and returns the same scientific visualization.

Usage

PlotZScore(
  data,
  TargetVar,
  variables,
  VariableCategories = NULL,
  Relabel = TRUE,
  sort = TRUE,
  RemoveXAxisLabels = TRUE,
  Ordinal = lifecycle::deprecated(),
  TreatOrdinalAs = "Continuous",
  Parametric = TRUE,
  SigP_YCoord = 1.5,
  SigFDR_YCoord = 1.6,
  Data = lifecycle::deprecated(),
  Variables = lifecycle::deprecated()
)

CreateZScorePlot(...)

Arguments

data

A dataframe containing the data to be analyzed.

TargetVar

A string specifying the column name of the grouping variable.

variables

A vector of strings specifying the column names of the variables to be analyzed.

VariableCategories

An optional vector categorizing the variables.

Relabel

Logical; if TRUE, variables will be relabeled using their labels from the dataframe.

sort

Logical; if TRUE, variables will be sorted by category and p-value.

RemoveXAxisLabels

Logical; if TRUE, X-axis labels will be removed.

Ordinal

Deprecated (since 20.20.0). Use TreatOrdinalAs instead.

TreatOrdinalAs

How ordinal variables are handled. This numeric plot accepts "Continuous" or "Exclude".

Parametric

Logical; if TRUE, parametric tests (t-test/ANOVA) will be used; otherwise, non-parametric tests (Wilcoxon/Kruskal-Wallis) will be used.

SigP_YCoord

Numeric; the y-coordinate for marking significant p-values.

SigFDR_YCoord

Numeric; the y-coordinate for marking significant FDR-adjusted p-values.

Data

Deprecated (since 19.15.0). Use data instead.

Variables

Deprecated (since 19.15.0). Use variables instead.

...

Arguments passed to PlotZScore().

Value

A ggplot object representing the Z-score plot.

Examples

data(SampleData)
data(SampleVariableTypes)

# Attach labels and factor levels for readable axis labels
Labelled <- RevalueData(SampleData, SampleVariableTypes)$RevaluedData

# Many variables, grouped into categories
vars <- c("AXL", "Adiponectin", "Alpha_1_Antitrypsin", "Alpha_2_Macroglobulin",
          "Apolipoprotein_A1", "Apolipoprotein_B", "C_Reactive_Protein",
          "Cortisol", "Cystatin_C", "Ferritin", "Insulin", "Leptin")
cats <- c(rep("Metabolic", 4), rep("Lipids", 2),
          rep("Inflammation", 3), rep("Endocrine", 3))

p <- PlotZScore(
  Labelled,
  TargetVar = "Diagnosis",
  variables = vars,
  VariableCategories = cats
)
p
#> Warning: Removed 5 rows containing missing values or values outside the scale range
#> (`geom_point()`).
#> Warning: Removed 8 rows containing missing values or values outside the scale range
#> (`geom_point()`).


# An interactive version via plotly
if (requireNamespace("plotly", quietly = TRUE)) {
  plotly::ggplotly(p)
}