CorrespondenceAnalysis: 'CorrespondenceAnalysis'

In Displayr/flipDimensionReduction: Algorithms for dimension reduction

CorrespondenceAnalysis

Description

Performs correspondence analysis to analyze a table or list of tables.

Usage

CorrespondenceAnalysis(
  x,
  normalization = "Principal",
  output = c("Scatterplot", "Bubble Chart", "Moonplot", "Text", "Input Table")[1],
  focus = NULL,
  supplementary = NULL,
  row.names.to.remove = c("NET", "Total", "SUM"),
  column.names.to.remove = c("NET", "Total", "SUM"),
  mirror.horizontal = FALSE,
  mirror.vertical = FALSE,
  color.palette = "Default colors",
  row.color = "#5B9BD5",
  col.color = "#ED7D31",
  bubble.size = NULL,
  bubble.title = "",
  chart.title = "Correspondence analysis",
  transpose = FALSE,
  logos = NULL,
  logo.size = 0.5,
  trend.lines = FALSE,
  show.gridlines = TRUE,
  multiple.tables = NA,
  square = FALSE,
  max.row.labels.plot = 200,
  max.col.labels.plot = 200,
  max.labels.plot = NA,
  dim1.plot = 1,
  dim2.plot = 2,
  title.font.size = 20,
  x.title.font.size = 16,
  y.title.font.size = 16,
  labels.font.size = 14,
  axis.font.size = 10,
  legend.font.size = 15,
  footer.wrap.length = 80,
  use.combined.scatter = FALSE,
  ...
)

Arguments

x	A matrix or a list of matrices.
normalization	The method used to normalize the coordinates of the correspondence analysis plot. The default method is "Principal", which plots the principal coordinates (i.e., the standard coordinates multiplied by the singular values). "Row principal" and "Column principal" plot the standard coordinates of the columns (rows) against the principal coordinates. "Row principal (scaled)" is the same as "Row principal" except that both column coordinates are equally scaled so that column points appear on a similar scale to row points. "Column principal (scaled)" is analagous. Note that the plotting occurs via print.CorrespondenceAnalysis.
output	How the map is displayed: "Scatterplot", "Moonplot", "Input Table", "Diagnostics", "Bubble Chart" or "Text".
focus	The label of a row or column category. The output is rotated so that the variance of this category lies along the first dimension.
supplementary	A vector of rows or columns to be treated as supplementary, i.e. not included in the calculation of the coordinate space but to be plotted.
row.names.to.remove	A vector of the row labels to remove.
column.names.to.remove	A vector of the column labels to remove.
mirror.horizontal	Boolean indicating whether to reverse the sign of values plotted along the horizontal axis.
mirror.vertical	Boolean indicating whether to reverse the sign of values plotted along the vertical axis.
color.palette	Palette used to color scatterplot when multiple tables are used.
row.color	Color to display row-attributes in scatterplot with one table.
col.color	Color to display column-attributes in scatterplot with one table.
bubble.size	A vector of magnitudes for the row coordinate (for bubble charts). This is optional.
bubble.title	A label for the legend.
chart.title	Title of chart.
transpose	Boolean indicating whether the rows and columns of x should be swapped.
logos	Optional list of images to be used to label scatterplot instead of the row names. It should be inputted as a comma-seperated list of URLs.
logo.size	Numeric controlling the size of the logos.
trend.lines	Boolean indicating whether to draw trend lines when multiple tables are supplied.
show.gridlines	Boolean indicating whether to show gridlines for "Scatterplot" and "Bubble Chart".
multiple.tables	Deprecated.
square	Boolean indicating whether the input table is square. If true the row and column names of the table must be the same.
max.row.labels.plot	A number specifying the maximum of row labels shown in bubble or scatterplots. The remaining rows will be shown with labels hidden.
max.col.labels.plot	A number specifying the maximum number column labels shown.
max.labels.plot	Deprecated. Use max.row.labels.plot instead.
dim1.plot	Dimension to show in X-axis of bubble or scatterplot.
dim2.plot	Dimension to show in Y-axis of bubble or scatterplot.
title.font.size	Font size of the chart title.
x.title.font.size	Font size of the horizontal axis title.
y.title.font.size	Font size of the vertical axis title.
labels.font.size	Font size of the labels on the scatterplot.
axis.font.size	Font size of the labels on the x- and y-axis.
legend.font.size	Font size of the legend.
footer.wrap.length	Maximum number of characters in the footer. If longer, the text will be wrapped.
use.combined.scatter	Draw scatterplots using rhtmlCombinedScatter.
...	Optional arguments for ca.

Displayr/flipDimensionReduction documentation built on Aug. 19, 2024, 9:29 p.m.