Package 'gg4way'

airwayFit data

Description

Generate example data from the airway data package using eBayes

Usage

data(airwayFit)

Format

An object of class MArrayLM with 14516 rows and 2 columns.

Value

A MArrayLM

Source

airway

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Helper Functions for gg4way

Description

These helper functions provide data used in the plot:

getCor	Get the correlation of the logFC of all genes
getShared	Get only the shared genes that pass the thresholds
getTotals	Get the totals of overlap categories

Usage

getCor(p1)

getShared(p1)

getTotals(p1)

Arguments

p1	The plot from gg4way

Value

Each function returns a different result:

getCor	A numeric
getShared	A tibble
getTotals	A tabyl

Examples

data("airwayFit")
p1 <- airwayFit |>
    gg4way(x = "N61311 vs N052611",
           y = "N061011 vs N052611")

## Correlation
getCor(p1)

## Shared
getShared(p1)

## Totals
getTotals(p1)

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Create a 4way plot

Description

Create a 4way plot to compare the logFC values from two contrasts of differential gene expression.

Usage

## Default S3 method:
gg4way(
  DGEdata,
  x = NULL,
  y = NULL,
  ID = "ID",
  symbol = "symbol",
  logFC = "logFC",
  FDR = "adj.P.Val",
  sep = " vs ",
  FDRcutoff = 0.05,
  logFCcutoff = 1,
  label = FALSE,
  colorVector = c("grey80", "firebrick", "forestgreen", "mediumblue"),
  lineColor = "grey60",
  textSize = 4,
  textNudge = 0.25,
  ...
)

Arguments

DGEdata	The object to plot from: limma: A MArrayLM object from eBayes or treat edgeR: A list of DGELRT objects from glmQLFTest, glmTreat, or glmLRT DESeq2: a DESeqDataSet from DESeq or a list of DESeqResults from results Other packages: A list of data.frames, see details section for more information
x	Character specifying the name of DGE results within the object for the x-axis
y	Character specifying the name of DGE results within the object for the y-axis
ID	Column name for gene IDs
symbol	Column name for gene symbols, which can be the same as the value for the ID column if not present in the object
logFC	Column name for logFC values
FDR	Column name for FDR values
sep	Character specifying the separator between conditions for the contrast name provided to the x and y arguments
FDRcutoff	Numeric for the FDR cut-off for DEGs (default is 0.05)
logFCcutoff	Numeric for the absolute logFC cut-off for DEGs (default is 1)
label	Character vector specifying the symbols of genes to label (FALSE for none, TRUE for all blue)
colorVector	Character vector of colors in the following order: "not significant", "significant in x", "significant in y", "significant in both"
lineColor	Color of lines
textSize	Numeric specifying size of text with gene overlap category totals, where 0 will remove the text
textNudge	Numeric specifying nudge of text with gene overlap category totals
...	Support for additional arguments used internally by gg4way.MArrayLM, gg4way.list, and gg4way.DESeqDataSet

Details

When a named list of data.frames is provided to the DGEdata argument, each data.frame can follow the defaults and have the following columns or specify alternate names for the following to the ID, symbol, logFC, and FDR arguments:

ID	Character vector with the feature ID (i.e. EnsemblID)
symbol	Optional character vector with gene symbol for labels
logFC	Numeric with the logFC
adj.P.Val	Numeric with the FDR

The correlation coefficient is useful for comparing across multiple plots. However, it is important to consider whether there are any common factors when comparing values, since that can result in a larger value. Some examples are contrasts with covariates that are shared between groups or contrasts with the same control group.

Value

A ggplot

Examples

data("airwayFit")
airwayFit |>
    gg4way(x = "N61311 vs N052611",
           y = "N061011 vs N052611")

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