Package 'CAbiplot'

Title: Correspondence Analysis Biplots and Diagnostic Reports
Description: A convenience wrapper around 'FactoMineR' and 'factoextra' for running Correspondence Analysis (CA) on a numeric data table (e.g. a genotype-by-trait or contingency-style matrix) and producing a full set of publication-ready diagnostic plots: scree plot, symmetric biplot, row-only and column-only plots, row/column contribution plots, and row/column cos2 (quality-of-representation) plots. A single top-level function runs the whole pipeline, prints formatted result tables, and optionally saves every plot as a high-resolution image, mirroring a typical CA reporting workflow used in agronomy and plant-breeding studies. An example genotype-by-trait data set is included.
Authors: Prakash Kumar [aut, cre], Himadri Sekhar Roy [aut], Ranjit Kumar Paul [aut], Md. Yeasin [aut], Sunil Kumar Yadav [aut], Amrit Kumar Paul [aut]
Maintainer: Prakash Kumar <[email protected]>
License: MIT + file LICENSE
Version: 0.1.0
Built: 2026-09-24 19:26:37 UTC
Source: https://github.com/cran/CAbiplot

Help Index

Symmetric CA biplot (rows and columns)

Description

Symmetric CA biplot (rows and columns)

Usage

ca_biplot(res.ca, axes = c(1, 2), col.row = "#1F4E79",
  col.col = "#B22222", ...)

Arguments

res.ca

An object of class "CA" from run_ca or CA.
axes

Length-2 integer vector of the dimensions to plot. Defaults to c(1, 2).
col.row

Color for row points/labels. Defaults to "#1F4E79".
col.col

Color for column points/labels. Defaults to "#B22222".
...

Additional arguments passed to fviz_ca_biplot.

Value

A ggplot object.

CA column-only plot

Description

CA column-only plot

Usage

ca_col_plot(res.ca, axes = c(1, 2), col.col = "#B22222", ...)

Arguments

res.ca

An object of class "CA" from run_ca or CA.
axes

Length-2 integer vector of the dimensions to plot. Defaults to c(1, 2).
col.col

Color for column points/labels. Defaults to "#B22222".
...

Additional arguments passed to fviz_ca_col.

Value

A ggplot object.

Row or column contribution plot

Description

Row or column contribution plot

Usage

ca_contrib_plot(res.ca, choice = c("row", "col"), axes = 1, top = NULL, ...)

Arguments

res.ca

An object of class "CA" from run_ca or CA.
choice

Either "row" or "col".
axes

Integer vector of dimension(s) to sum contributions over. Defaults to 1.
top

Number of rows/columns to display. Defaults to all of them.
...

Additional arguments passed to fviz_contrib.

Value

A ggplot object.

Row or column cos2 (quality of representation) plot

Description

Row or column cos2 (quality of representation) plot

Usage

ca_cos2_plot(res.ca, choice = c("row", "col"), axes = 1:2, top = NULL, ...)

Arguments

res.ca

An object of class "CA" from run_ca or CA.
choice

Either "row" or "col".
axes

Integer vector of dimension(s) to sum cos2 over. Defaults to 1:2.
top

Number of rows/columns to display. Defaults to all of them.
...

Additional arguments passed to fviz_cos2.

Value

A ggplot object.

Run a full Correspondence Analysis report

Description

End-to-end pipeline that runs Correspondence Analysis on data and produces the full battery of diagnostic plots used in the package vignette: a scree plot, a symmetric biplot, row-only and column-only plots, row and column contribution plots (dimensions 1 and 2), row and column cos2 plots, and a combined summary figure. Optionally saves every plot as a high-resolution JPEG and prints formatted result tables to the console, mirroring a typical CA reporting workflow.

Usage

ca_report(data, output_dir = ".", prefix = "CA", save_plots = TRUE,
  dpi = 600, verbose = TRUE)

Arguments

data

A numeric matrix, numeric data.frame, a path to a delimited text file, or an already-computed object of class "CA".
output_dir

Directory where plots are saved when save_plots = TRUE. Created if it does not already exist. Defaults to the current working directory.
prefix

File name prefix used for saved plots. Defaults to "CA".
save_plots

Logical; save each plot as a JPEG in output_dir? Defaults to TRUE.
dpi

Resolution (dots per inch) used when saving plots. Defaults to 600.
verbose

Logical; print formatted result tables (eigenvalues, coordinates, contributions, cos2) to the console? Defaults to TRUE.

Value

Invisibly, a list with elements:

res.ca

The fitted "CA" object.

eig

Eigenvalue/inertia table from get_eigenvalue.

plots

A named list of the individual ggplot objects (scree, biplot, row, col, contrib_row_dim1, contrib_row_dim2, contrib_col_dim1, contrib_col_dim2, cos2_row, cos2_col) plus combined, a gridExtra arrangement of the scree plot, biplot, and the two dimension-1 contribution plots.

Examples

geno <- get_genotype_traits()
report <- ca_report(geno, save_plots = FALSE, verbose = FALSE)
report$plots$biplot

CA row-only plot

Description

CA row-only plot

Usage

ca_row_plot(res.ca, axes = c(1, 2), col.row = "#1F4E79", ...)

Arguments

res.ca

An object of class "CA" from run_ca or CA.
axes

Length-2 integer vector of the dimensions to plot. Defaults to c(1, 2).
col.row

Color for row points/labels. Defaults to "#1F4E79".
...

Additional arguments passed to fviz_ca_row.

Value

A ggplot object.

Scree plot of CA eigenvalues

Description

Scree plot of CA eigenvalues

Usage

ca_scree_plot(res.ca, ...)

Arguments

res.ca

An object of class "CA" from run_ca or CA.
...

Additional arguments passed to fviz_eig.

Value

A ggplot object.

Load the bundled example genotype-by-trait data set

Description

Loads the example data set shipped with the package: a table of plant genotypes (rows) evaluated across six morphological/agronomic traits (columns). This is the same data used in the package vignette and examples.

Usage

get_genotype_traits()

Value

A numeric data.frame with genotypes as row names and traits as columns.

Examples

geno <- get_genotype_traits()
head(geno)

Read a CA-ready numeric data table

Description

Reads a delimited text file into a numeric data.frame suitable for CA. The first column is used as row names, and every remaining column is coerced to numeric.

Usage

read_ca_data(file, sep = ",", header = TRUE, row.names = 1,
  check.names = FALSE)

Arguments

file

Path to a delimited text file (e.g. CSV).
sep

Field separator passed to read.table. Defaults to ",".
header

Logical; does the file have a header row? Defaults to TRUE.
row.names

Column to use as row names, passed to read.table. Defaults to 1 (the first column).
check.names

Logical; passed to read.table. Defaults to FALSE so that column names are kept exactly as written in the file.

Value

A numeric data.frame with row names taken from the input file.

Examples

file <- system.file("extdata", "genotype_traits.csv", package = "CAbiplot")
data <- read_ca_data(file)
head(data)

Run Correspondence Analysis on a numeric data table

Description

Thin, validating wrapper around CA. Accepts either a numeric matrix/data.frame already in memory, or a path to a delimited text file, which is read with read_ca_data.

Usage

run_ca(data, ...)

Arguments

data

A numeric matrix, numeric data.frame, or a path (character string) to a delimited text file to be read with read_ca_data.
...

Additional arguments passed on to CA (for example ncp, row.sup, col.sup).

Value

An object of class "CA" as returned by CA, computed with graph = FALSE.

Examples

geno <- get_genotype_traits()
res.ca <- run_ca(geno)
summary(res.ca)