Creates all the partial ggplot2 maps for CA with all standard variants of normalization for factor scores.

createAllMaps4CA: uses ggplot2 to

create all the partial maps for CA with the different types of normalizations: Asymmetric, Symmetric, True-Barycentric, Biplots, and SPSS pseudo Biplots.

to creates ggplot2 factorial maps for dots and labels; 3) to create the base plot maps for CA type graphs, and 4) to creates maps for the \(I\) (rows) and the \(J\) (column) -sets.

Usage

createAllMaps4CA(
  allNormedFactors,
  axis1 = 1,
  axis2 = 2,
  title = NULL,
  col.points.i = "blueviolet",
  alpha.points.i = 0.5,
  pch.i = 19,
  cex.i = 2.5,
  segment.size.i = 0,
  col.labels.i = "darkorchid4",
  alpha.labels.i = 1,
  text.cex.i = 4,
  font.face.i = "bold",
  font.family.i = "sans",
  force.i = 1,
  col.points.j = "darkolivegreen4",
  alpha.points.j = 0.5,
  pch.j = 18,
  cex.j = 2.5,
  segment.size.j = 0,
  col.labels.j = "darkolivegreen",
  alpha.labels.j = 1,
  text.cex.j = 4,
  font.face.j = "bold",
  font.family.j = "sans",
  force.j = 1,
  col.axes = "darkorchid",
  alpha.axes = 0.2,
  width.axes = 1.1,
  col.background = adjustcolor("lavender", alpha.f = 0.2),
  ...
)

Arguments

allNormedFactors,: A list with all the factor scores normed typically from createAllNormedFactors.
axis1: the column of X used for the horizontal axis of the plot. Default = 1.
axis2: the column of X used for the vertical axis of the plot. Default = 2.
title: A main title (default is NULL).
col.points.i: the color of the points/dots for the \(I\)-set. Can be one color or a vector of colors. If a vector, it needs to have exactly the number of items to be plotted. Default = 'blueviolet'.
alpha.points.i: (default = .5), the alpha (transparency) for the points, should be between 1 (opaque) and 0 (completely transparent).
pch.i: the character for the points for the \(I\)-set. Default is 19 (Circles).
cex.i: size of the dots for the \(I\)-set. Default = 2.5
segment.size.i: = 0, # size of segment
col.labels.i: the color of the labels for the \(I\)-set. Can be one color or a vector of colors. If a vector, it needs to have exactly the number of items to be plotted. Default = 'darkorchid'.
alpha.labels.i: (default = 1), the alpha (transparency) for the labels, should be between 1 (opaque) and 0 (completely transparent).
text.cex.i: = 4, font size for labels for the I-set.
font.face.i: (Default = 'bold') font for labels for the \(I\)-set.
font.family.i: (Default = 'sans') font family for the \(I\)-set.
force.i: (Default = 1) How much ggrepel repels the labels for the \(I\)-set.
col.points.j: the color of the points/dots for the \(J\)-set. Can be one color or a vector of colors. If a vector, it needs to have exactly the number of items to be plotted. Default = 'darkolivegreen4'.
alpha.points.j: (Default = .5), the alpha (transparency) for the \(J\)-points, should be between 1 (opaque) and 0 (completely transparent).
pch.j: the character for the points for the \(J\)-set. Default is 18 (Diamonds).
cex.j: size of the dots for the \(J\)-set. Default = 2.5
segment.size.j: = 0, # size of segment for \(J\)-set
col.labels.j: the color of the labels for the \(J\)-set. Can be one color or a vector of colors. If a vector, it needs to have exactly the number of items to be plotted. Default = 'darkolivegreen'.
alpha.labels.j: (default = 1), the alpha (transparency) for the \(J\)-labels, should be between 1 (opaque) and 0 (completely transparent).
text.cex.j: (Default = 4) font size for labels for the \(J\)-set.
font.face.j: (Default = 'bold' font for the labels for the \(J\)-set.
font.family.j: (Default = 'sans') font family for the \(J\)-set.
force.j: (Default = 1). How much ggrepel repels the labels for the \(J\)-set.
col.axes: (Default = 'darkorchid') color for the axes.
alpha.axes: (Default = .2) transparency factor for the color of the axes.
width.axes: (Default = 1.1) the width of the axes
col.background: Default = adjustcolor('lavender', alpha.f = .2), The color of the background.
...: eveythings else for the functions.

Value

a list with baseMap_S: The Background (Symmetric) I_labels_S The labels I-set (Symmetric). I_points_S The dots I-set (Symmetric). J_labels_S The labels J-set (Symmetric). J_points_S The dots J-set(Symmetric). baseMap_A The Background (Asymmetric) I_labels_A The labels I-set (Asymmetric). I_points_A The dots I-set (Asymmetric). J_labels_A The labels J-set (Asymmetric). J_points_A The dots J-set (Asymmetric). baseMap_B The Background (Barycentric). I_labels_B The labels I-set (Barycentric). I_points_B The dots I-set (Barycentric). J_labels_B The labels J-set (Barycentric). J_points_B The dots J-set (Barycentric).

Details

The final maps are built by combining the elementary maps. For example, a map with the \(J\)-set being asymmetric and the \(I\)-set being Symmetric would be made by creating the Ja_Is map as Ja_Is <- baseMap_A + J_labels_A + I_labels_S.

Note than, in general, the Asymmetric is larger than the Symmetric map which is in turn larger than the Barycentric map.

Important_Note

When creating multiple layers graphs, because of the way ggplot2 create graphs, all the matrices/dataframe should all the have the same column names e.g., jB2U5NTSJy7CWf8zaM16G05cmn6fyLsv-2- equal to c("Dimension 1", "Dimension 2"). When this is not the case, some strange and cryptic errors may be produced (e.g., "cannot find Dimension").

Author