R/CreateFactorMaps4CA.R
In HerveAbdi/PTCA4CATA: Partial Triadic Analysis (PTCA) for Check All That Apply (CATA) Data
Defines functions
createAllMaps4CA
createFactorMapIJ
map4DotsAndLabels
print.createFactorMap
createFactorMap
createBaseMap
Documented in
createAllMaps4CA
createBaseMap
createFactorMap
createFactorMapIJ
map4DotsAndLabels
print.createFactorMap
# Preamble ----
#********************************************************************
#_____________________________________________________________________
# function for creating Factor Based Map
# createBaseMap
# createFactorMap
# map4DotsAndLabels
#
# Revision October/21/2017. in createFactorMap
# fix problem with axis different from 1 and 2
#
#_____________________________________________________________________
# function: createBaseMap
# createBaseMap ----
#_____________________________________________________________________
#' create a base map for CA type graphs with ggplot2
#'
#' \code{createBaseMap}: Create a ggplot2 basemap for CA type graphs.
#' The final maps are created by using overlays.
#' A map CA is created with first the baseMap and
#' then adding a text/dot map.
#' @seealso \code{\link{createFactorMapIJ}}
#' @param data the factor scores to plot
#' @param constraints a list with minx miny maxx maxy
#' typically obtained from \code{prettyGraphs::minmaxHelper()}.
#' If \code{NULL}
#' (default) it is computed with the function
#' \code{prettyGraphs::minmaxHelper()}.
#' @param col.axes color for the axes, default is
#' \code{'darkorchid'}.
#' @param alpha.axes alpha parametere (transparency)
#' for the axes, default is .2.
#' @param width.axes the width of the axes, default is 1.1.
#' @param col.background the color theme of the background,
#' default is \code{adjustcolor('lavender', alpha.f = .2)}.
#' @param title a main title, default is \code{NULL} (no title)
#' @return a basemap
#' @import prettyGraphs ggplot2 grDevices
#' @export
#' @author Hervé Abdi
#' @section Important_Note: When creating multiple layers graphs,
#' because of the way \code{ggplot2} create graphs, all the
#' the matrices/dataframe should all the have the same column names
#' [e.g., \code{colnames()} equal to
#' \code{c("Dimension 1", "Dimension 2")}].
#' When it is not the case, some strange and cryptic
#' error may be produced
#' (e.g., \code{"cannot find Dimension"}).
#' @examples \dontrun{
#' aBaseMap <- createBaseMap(Fi)
#' # with Fi being a map of factor scores
#' }
createBaseMap <- function(data,
constraints = NULL,
col.axes = 'darkorchid',
alpha.axes = .2,
width.axes = 1.1,
col.background =
adjustcolor('lavender',
alpha.f = .2),
title = NULL){
if (is.null(col.background)){col.background = 'transparent'}
data <- as.data.frame(data)
if (is.null(constraints)) {
# lapply(prettyGraphs::minmaxHelper(Fj[,3:4]),'*',1.1)
constraints <- lapply(prettyGraphs::minmaxHelper(data),'*',1.1)
}
V1 = as.name(colnames(data)[1])
V2 = as.name(colnames(data)[2])
# Create a Background Map
LeG_b <- ggplot(data = data,
# aes(data[,1],data[2])
aes_string(V1, V2)
) +
coord_fixed(ratio = 1)
LeG_b = LeG_b +
xlim(constraints$minx,constraints$maxx) +
ylim(constraints$miny,constraints$maxy)
LeG_b <- LeG_b + geom_hline(yintercept = 0, size = width.axes,
color = col.axes,alpha = alpha.axes) +
geom_vline(xintercept = 0, size = width.axes ,
color = col.axes,alpha = alpha.axes) +
theme(panel.background = element_rect(fill = col.background,
color = col.axes))
if (!is.null(title))LeG_b <- LeG_b + ggtitle(title)
return(LeG_b)
}
# End of function createBaseMap
#_____________________________________________________________________
# function: createFactorMap
#_____________________________________________________________________
# createFactorMap ----
# create the base plot for factor type plots
# gives a baseMap and one map for dots and one map for labels
#_____________________________________________________________________
#' @title create the base plot maps for CA type
#' graphs with \code{ggplot2}.
#'
#' @description \code{createFactorMap}:
#' Creates the \code{ggplot2} basic factor maps for CA type graphs.
#' The final maps are created by using overlays on top of the base map.
#'
#' A map for CA is created with the baseMap to which
#' is added text/dot map.
#' \code{createFactorMap} calls the functions \code{map4DotsAndLabels}
#' and \code{createBaseMap}.
#'
#' @seealso \code{\link{map4DotsAndLabels}}
#' \code{\link{createBaseMap}}
#' .
#' @param X the factor scores to plot.
#' @param axis1 the column of X used for the horizontal axis
#' of the plot. Default = 1.
#' @param axis2 the column of X used for the vertical axis
#' of the plot. Default = 2.
#' @param constraints a list with \code{minx miny maxx maxy},
#' typically obtained from \code{ExPosition}. If \code{NULL}
#' (default) it is computed with the function
#' \code{prettyGraphs::minmaxHelper()}.
#' @param title A title for the graph. Default is \code{NULL}.
#' @param col.points the color of the points/dots.
#' 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 = \code{'blueviolet'}.
#' @param alpha.points (default = .5), the alpha
#' (transparency) for the points, should be
#' between 1 (opaque) and 0
#' (completely transparent).
#' @param display.points if \code{TRUE} (Default)
#' create the map for the points.
#' @param pch the character for the points,
#' Default is 19 (circles).
#' @param cex size of the dots. Default = 2.5
#' @param display.labels if \code{TRUE} (Default),
#' create the
#' map for the labels.
#' @param col.labels the color of the labels
#' 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 = \code{'darkorchid'}.
#' @param alpha.labels (default = 1), the alpha
#' (transparency) for the points, should be
#' between 1 (no transparency) and 0
#' (completely transparent).
#' @param text.cex = 4, font size for labels.
#' @param font.face (Default = \code{'bold'}) font for labels.
#' @param font.family (Default = \code{'sans'})
#' font family for labels.
#' @param col.axes color for the axes, default is
#' \code{'darkorchid'}.
#' @param alpha.axes alpha parameter (transparency)
#' for the axes, default is .2.
#' @param width.axes the width of the axes, default is 1.1.
#' @param col.background the color theme of the background,
#' default is \code{adjustcolor('lavender', alpha.f = .2)}.
#' @param force \code{(default = 1)}.
#' How much \code{ggrepel} repels the label
#' @param segment.size \code{(default = 0)}
#' size of segment line for \code{ggrpel}.
#' @param ... stuff to be passed to other functions.
#' @return a list with 6 elements:
#' \enumerate{
#' \item \code{zeMap}: The Complete Map (background Dots and Labels);
#' \item \code{zeMap_background}: The Background;
#' \item \code{zeMap_dots:}: The dots;
#' \item \code{zeMap_text:}: The Labels;
#' \item \code{factorScores:}: The factor scores; and
#' \item \code{constraints:}: The list of the contraints'
#' }
#; NB class = \code{'createFactorMap'}.
#' @section Important_Note: When creating multiple layers graphs,
#' because of the way \code{ggplot2} create graphs, all
#' the matrices/dataframe should all the have the same column names
#' [e.g., \code{colnames()} equal to
#' \code{c("Dimension 1", "Dimension 2")}].
#' When it is not the case, some strange and cryptic
#' error may be produced
#' (e.g., \code{"cannot find Dimension"}).
#' @import prettyGraphs grDevices
#' @export
# @examples \dontrun{}
#' @author Hervé Abdi
createFactorMap <- function(X,
axis1 = 1, axis2 = 2,
constraints = NULL,
# list with minx miny maxx maxy
# as obtained, e.g.,
# from minmacHelper from prettyGraphs
title = NULL,
col.points = 'blueviolet',
alpha.points = .5,
display.points = TRUE,
pch = 19, # Character for the dots
cex = 2.5, # size of the dots
display.labels = TRUE,
col.labels = 'darkorchid4',
alpha.labels = 1,
text.cex = 4, # font size for labels
font.face = 'bold', # font for labels
font.family = 'sans' ,
# font family for labels
col.axes = 'darkorchid',
# color for the axes
alpha.axes = .2,
# tranparency for the axes
width.axes = 1.1,
# width of the axes
col.background =
adjustcolor('lavender',
alpha.f = .2),
force = 1, # for ggrepel
segment.size = 0, # size of segment line
# background color
... # more stuff
){ #col.labels <- ggplot2::alpha(col.labels, alpha = alpha.labels)
#col.points <- ggplot2::alpha(col.points, alpha = alpha.points)
#
if (is.null(title)){title = ''}
#
# give a name to the Dimension of Fi is there is none
if (is.null(colnames(X))){
colnames(X) <- paste0('Dimension ',1:ncol(X))
}
# G = as.data.frame(X[,c(axis1,axis2)])
G = as.data.frame(X)
#V1 = as.name(colnames(G)[1])
#V2 = as.name(colnames(G)[2])
# NB default uses minmaxHelper from prettyPlots
if (is.null(constraints)){
constraints <-
lapply(prettyGraphs::minmaxHelper(G[,c(axis1,axis2)]),'*',1.1)
}
#
#___________________________________________________________________
# NB geom_text_repel is from ggrepel
LeG_b <- createBaseMap(data = G[,c(axis1,axis2)],
constraints = constraints,
col.axes = col.axes, # 'darkorchid',
alpha.axes = alpha.axes,
width.axes = width.axes,
col.background = col.background,
title = title)
LesG_dl <- map4DotsAndLabels(
data = G[,c(axis1,axis2)],
axis1 = 1,
axis2 = 2,
display.points = display.points,
col.points = col.points,
alpha.points = alpha.points,
pch = pch,
# Character for the points
cex = cex,
# size of the points
display.labels = display.labels,
col.labels = col.labels,
alpha.labels = alpha.labels,
text.cex = text.cex,
# font size for labels
font.face = font.face, #'bold',
# font for labels
font.family = font.family ,'sans',
# font family for labels
# below are ggrepel values
force = force, # labels' repulsion for ggrepel
segment.size = segment.size,
# segment width for ggrepel
nudge_x = 0,
nudge_y = 0 # from ggrepel
# nudge value for starting point for
# labels (ggrepel)
, ... # in case we need more stuff for ggrepel
)
LeG = LeG_b
if (display.points){LeG = LeG + LesG_dl$leG.points}
if (display.labels){LeG = LeG + LesG_dl$leG.labels}
return.list <- structure(list(zeMap = LeG,
zeMap_background = LeG_b,
zeMap_dots = LesG_dl$leG.points,
zeMap_text = LesG_dl$leG.labels,
factorScores = G, constraints = constraints),
class = 'createFactorMap')
return(return.list)
#
} # End of Function
#_____________________________________________________________________
#' Change the print function for \code{createFactorMap}
#'
#' Change the print function for objsects of the
#' class \code{createFactorMap}
#'
#' @param x a list: output of \code{createFactorMap}
#' @param ... everything else for the functions
#' @author Herve Abdi
#' @export
print.createFactorMap <- function(x, ...) {
ndash = 78 # How many dashes for separation lines
cat(rep("-", ndash), sep = "")
cat("\nBasic Factor Maps (with ggplot2) \n")
# cat("\n List name: ",deparse(eval(substitute(substitute(x)))),"\n")
cat(rep("-", ndash), sep = "")
cat("\n$zeMap ", "A standard map with background, points, and Labels")
cat("\n$zeMap_background ", "The background map")
cat("\n$zeMap_dots ", "The points map")
cat("\n$zeMap_text ", "The labels map")
cat("\n$factorScores ", "The factor scores (coordinates)")
cat("\n$constraints ", "map constraints (a list with minx miny maxx maxy)")
cat("\n",rep("-", ndash), sep = "")
cat("\n")
invisible(x)
} # end of function print.createNormedFactors
#_____________________________________________________________________
#_____________________________________________________________________
# function: map4DotsAndLabels ----
#_____________________________________________________________________
#' Create \code{ggplot2} factorial maps for dots and labels.
#'NB needs a base map to work correctly
#'
#' \code{map4DotsAndLabels}:
#' Creates \code{ggplot2} factorial map for dots and labels.
#'NB: needs a base map to work correctly.
#' create the base plot maps for CA type graphs with \code{ggplot2}
#'
#' @param data the factor scores to plot
#' @param axis1 the column of X used for the horizontal axis
#' of the plot. \code{Default 1}.
#' @param axis2 the column of \code{X} used for the vertical axis
#' of the plot. \code{Default 2}.
#' @param display.points if \code{TRUE} (Default)
#' create the map for the points.
#' @param col.points the color of the points/dots.
#' Can be one color or a vector of colors. If a vector it needs
#' to have exactly the number of items to be plotted.
#' \code{Default = 'blueviolet'}.
#' @param alpha.points \code{(default = .5)}, the alpha
#' (transparency) for the points, should be
#' between 1 (no transparency) and 0
#' (completely transparent).
#' @param pch the character for the points,
#' Default is 19 (Circles).
#' @param cex size of the dots. Default = 2.5
#' @param display.labels if \code{TRUE} (default), create the
#' map for the labels.
#' @param col.labels the color of the labels
#' 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 = \code{'darkorchid'}.
#' @param alpha.labels (default = 1), the alpha
#' (transparency) for the labels, should be
#' between 1 (no transparency) and 0
#' (completely transparent).
#' @param force = 1. How much \code{ggrepel} repels the labels.
#' @param segment.size = 0,
#' size of segment line for \code{ggrpel}.
#' @param text.cex = 4, font size for labels.
#' @param font.face (default = \code{'bold'}) font for labels.
#' @param font.family (default = \code{'sans'}),
#' font family for labels.
#' @param nudge_x (default = 0). From \code{ggrepel},
#' nudge value for starting point for
#' labels: x dimension.
#' @param nudge_y (default = 0). From \code{ggrepel},
#' nudge value for starting point for
#' labels: y dimension.
#' @param alpha.point (default = .5), the alpha
#' (transparency) for the points, should be
#' between 1 (no transparency) and 0
#' (completely transparent).
#' @param ... everything else to pass to the functions
#' @return a list with 6-elements:
#' \enumerate{
#' \item \code{zeMap}: The Complete Map (background Dots and Labels);
#' \item \code{zeMap_background}: The Background map;
#' \item \code{zeMap_dots:} The dots;
#' \item \code{zeMap_text:} The Labels;
#' \item \code{factorScores:} The factor scores; and
#' \item \code{constraints:} The list of the contraints
#' (could be used to generate other graphs
#' with the same scaling factors).
#' }
#; NB class = 'createFactorMap'
#' @section Important_Note: When creating multiple layers graphs,
#' because of the way \code{ggplot2} create graphs, all
#' the matrices/dataframe should all the have the same column names
#' [e.g., \code{colnames()} equal to
#' \code{c("Dimension 1", "Dimension 2")}].
#' When it is not the case, some strange and cryptic
#' error may be produced
#' (e.g., \code{"cannot find Dimension"}).
#' @import ggplot2 ggrepel
#' @export
#' @author Herve Abdi
#' @rdname map4DotsAndLabels
#' @seealso \code{\link{createFactorMap}} \code{\link{createBaseMap}}
map4DotsAndLabels <- function(data,
axis1 = 1, axis2 = 2,
display.points = TRUE,
col.points = 'blueviolet',
alpha.points = .5,
pch = 19, # Character for the points
cex = 2.5, # size of the points
display.labels = TRUE,
col.labels = 'darkorchid4',
alpha.labels = 1,
force = 1,
segment.size = 0,
# segment width for ggrepel
text.cex = 4,
# font size for labels
font.face = 'bold',
# font for labels
font.family = 'sans',
# font family for labels
nudge_x = 0, nudge_y = 0, # from ggrepel
# nudge value for starting point for
# labels
... # for ggrepel in case
){# function map4DotsAndLabels start here
data <- as.data.frame(data) # make sure that we a df
V1 = as.name(colnames(data)[1])
V2 = as.name(colnames(data)[2])
# Create the Dot-map
LeG_dot = NULL
if (display.points){
LeG_dot =
# Next describe the points
ggplot2::geom_point(
data = data,
aes_string(V1, V2),
shape = pch,
size = cex,
color = col.points,
alpha = alpha.points# ,alpha = .5
)
}
# Create the text-map
LeG_text = NULL
if (display.labels){
LeG_text = # The text
ggrepel::geom_text_repel(
label = rownames(data),
data = data,
aes_string(V1, V2),
#aes(G[,1],G[,2]),
segment.size = segment.size,
size = text.cex,
fontface = font.face,
family = font.family,
color = col.labels,
alpha = alpha.labels,
nudge_x = nudge_x,
nudge_y = nudge_y
)
}
return(list(leG.points = LeG_dot, leG.labels = LeG_text))
} # End of function.
# function map4DotsAndLabels ends here
#_____________________________________________________________________
#_____________________________________________________________________
#_____________________________________________________________________
# function: createFactorMapIJ
#_____________________________________________________________________
#' Create
#' ggplot2 factorial maps for CA-type of maps dots and labels.
#'
#' \code{createFactorMapIJ}: Creates
#' \code{ggplot2} factorial maps for dots and labels.
#'NB needs a base map to work correctly.
#'
#' @param Fi the \eqn{I}-set factor scores to plot
#' @param Fj the \eqn{J}-set factor scores to plot
#' @param axis1 the column of X used for the horizontal axis
#' of the plot. Default 1.
#' @param axis2 the column of X used for the vertical axis
#' of the plot. Default 2.
#' @param constraints a list with minx miny maxx maxy
#' typically obtained from \code{prettyGraphs::minmaxHelper()}.
#' If \code{NULL}
#' (default) it is computed with the function
#' \code{prettyGraphs::minmaxHelper()}.
#' @param title a title for the plots.
#' @param col.points.i the color of the points/dots for the \eqn{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 = \code{'blueviolet'}.
#' @param alpha.points.i (default = .5), the alpha
#' (transparency) for the points, should be
#' between 1 (no transparency) and 0
#' (completely transparent).
#' @param pch.i the character for the points for the \eqn{I}-set.
#' Default is 19 (Circles).
#' @param cex.i size of the dots for the \eqn{I}-set. Default = 2.5
#' @param col.labels.i the color of the labels for
#' the \eqn{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 = \code{'darkorchid'}.
#' @param alpha.labels.i (default = 1), the alpha
#' (transparency) for the \eqn{I}-labels, should be
#' between 1 (no transparency) and 0
#' (completely transparent).
#' @param text.cex.i = 4, font size for labels for the I-set.
#' @param segment.size.i = 0, # size of segment
#' @param font.face.i (Default = \code{'bold'},
#' font for labels for the \eqn{I}-set.
#' @param font.family.i (Default = \code{'sans'})
#' font family for the \eqn{I}-set.
#' @param force.i (Default = 1). How much ggrepel repels the labels
#' for the \eqn{I}-set.
#' @param col.points.j the color of the points/dots
#' for the \eqn{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 = \code{'darkolivegreen4'}.
#' @param alpha.points.j (default = .5), the alpha
#' (transparency) for the points, should be
#' between 1 (no transparency) and 0
#' (completely transparent).
#' @param pch.j the character for the points for the \code{J}-set.
#' Default is 18 (Diamonds).
#' @param cex.j size of the dots for the \eqn{J}-set. Default = 2.5
#' @param segment.size.j = 0, # size of segment for \eqn{J}-set
#' @param col.labels.j the color of the labels for
#' the \eqn{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 = \code{'darkolivegreen'}.
#' @param alpha.labels.j (default = 1), the alpha
#' (transparency) for the \eqn{J}-labels, should be
#' between 1 (no transparency) and 0
#' (completely transparent).
#' @param text.cex.j (Default = 4), font size for labels for the J-set.
#' @param font.face.j (Default = \code{'bold'}),
#' font for labels for the \eqn{J}-set.
#' @param font.family.j (Default = \code{'sans'})
#' font family for the \eqn{J}-set.
#' @param force.j = 1. How much ggrepel repels
#' the labels for the \eqn{J}-set.
#' @param col.axes (Default = \code{'darkorchid'})
#' color for the axes
#' @param alpha.axes (Default = .2) transoarency factors for the
#' color of the axes.
#' @param width.axes (Default = 1.1) the width of the axes
#' @param col.background [Default =
#' \code{adjustcolor('lavender', alpha.f = .2)}]
#' The color of the background.
#' @param nudge_x = 0. From \code{ggrepel},
#' nudge value for starting point for
#' labels: x dimension.
#' @param nudge_y = 0. From \code{ggrepel},
#' nudge value for starting point for
#' labels: y dimension.
#' @param ... everything else for the functions
#' @return a list with
#' 1) \code{zeMap:} The Complete Map (background Dots and Labels);
#' 2) \code{zeMap_background:} The background;
#' 3) \code{zeMap_dots:} The dots;
#' 4) \code{zeMap_text:} The labels;
#' 5) \code{factorScores}: The factor scores; and
#' 6) \code{constraints:} The list of the contraints.
#; NB class = 'createFactorMap'
#' @section Important_Note: When creating multiple layers graphs,
#' because of the way \code{ggplot2} creates graphs, all the
#' the matrices/dataframe should all the have the same column names
#' [e.g., \code{colnames()} equal to c("Dimension 1", "Dimension 2")].
#' When it is not the case, some strange and cryptic
#' error may be produced
#' (e.g., "cannot find Dimension").
#' @import prettyGraphs
#' @export
# @examples \dontrun{}
#' @author Herve Abdi
#' @seealso createFactorMaps createbaseMap
# Function
# createFactorMapIJ
# createFactorMapIJ
# create the base plot for factor type plots
# give a baseMap and one map for dots and one map for labels
#
createFactorMapIJ <- function(Fi,Fj,
axis1 = 1, axis2 = 2,
constraints = NULL,
# list with minx miny maxx maxy
# as obtained, e.g.,
# from minmacHelper from prettyGraphs
title = NULL,
# The I-set
col.points.i = 'blueviolet',
alpha.points.i = .5,
# display.points.i = TRUE,
pch.i = 19, # Character for the dots
cex.i = 2.5, # size of the dots
segment.size.i = 0, # size of segment
# display.labels.i = TRUE,
col.labels.i = 'darkorchid4',
alpha.labels.i = 1,
text.cex.i = 4, # font size for labels
font.face.i = 'bold', # font for labels
font.family.i = 'sans' ,
force.i = 1 , # force repel factor for ggrepel
# The J-set
col.points.j = 'darkolivegreen4',
#display.points.j = TRUE,
alpha.points.j = .5,
pch.j = 18, # Character for the dots
cex.j = 2.5, # size of the dots
segment.size.j = 0, # size of segment
#display.labels.j = TRUE,
col.labels.j = 'darkolivegreen',
alpha.labels.j = .5,
text.cex.j = 4, # font size for labels
font.face.j = 'bold', # font for labels
font.family.j = 'sans' ,
force.j = 1 , # force repel factor for ggrepel
# font family for labels
col.axes = 'darkorchid',
# color for the axes
alpha.axes = .2,
# transparency for the axes
width.axes = 1.1,
# width of the axes
col.background =
adjustcolor('lavender',
alpha.f = .2),
# background color
nudge_x = 0,
nudge_y = 0,
... # more stuff
){
#
if (is.null(title)){title = ''}
# Use ggplot from ggplot2
#
Fi <- as.data.frame( Fi[,c(axis1,axis2)])
Fj <- as.data.frame( Fj[,c(axis1,axis2)])
# give a name to the Dimension of Fi is there is none
if (is.null(colnames(Fi))){
colnames(Fi) <- paste0('Dimension ',1:ncol(Fi))
colnames(Fj) <- paste0('Dimension ',1:ncol(Fj))
}
# G = as.data.frame(Fi[,c(axis1,axis2)])
#V1 = as.name(colnames(G)[1])
#V2 = as.name(colnames(G)[2])
# NB default uses minmaxHelper from prettyPlots
if (is.null(constraints)){
constraints <-
lapply(prettyGraphs::minmaxHelper(Fi,Fj),'*',1.1)
}
#___________________________________________________________________
# First the basemao
LeG_b <- createBaseMap(data = rbind(Fi,Fj),
constraints = constraints,
col.axes = col.axes, # 'darkorchid',
alpha.axes = alpha.axes,
width.axes = width.axes,
col.background = col.background,
title = title)
# dots and labels map
LesGi_dl <- map4DotsAndLabels(
data = Fi,
axis1 = 1,
axis2 = 2,
# display.points = TRUE,
col.points = col.points.i,
alpha.points.i = alpha.points.i,
pch = pch.i,
# Character for the points
cex = cex.i,
# size of the points
#display.labels = display.labels,
col.labels = col.labels.i,
alpha.labels.i = alpha.labels.i,
text.cex = text.cex.i,
# font size for labels
font.face = font.face.i, #'bold',
# font for labels
font.family = font.family.i , # 'sans',
# font family for labels
# below are ggrepel values
force = force.i, # labels' repulsion for ggrepel
segment.size = segment.size.i,
# segment width for ggrepel
nudge_x = nudge_x ,
nudge_y = nudge_y # from ggrepel
# nudge value for starting point for
# labels (ggrepel)
, ... # in case we need more stuff for ggrepel
)
LesGj_dl <- map4DotsAndLabels(
data = Fj,
axis1 = 1,
axis2 = 2,
#display.points = display.points,
col.points = col.points.j,
alpha.points.j = alpha.points.j,
pch = pch.j,
# Character for the points
cex = cex.j,
# size of the points
#display.labels = display.labels,
col.labels = col.labels.j,
alpha.points.j = alpha.points.j,
text.cex = text.cex.j,
# font size for labels
font.face = font.face.j, #'bold',
# font for labels
font.family = font.family.j ,# 'sans',
# font family for labels
# below are ggrepel values
force = force.j, # labels' repulsion for ggrepel
segment.size = segment.size.j,
# segment width for ggrepel
nudge_x = nudge_x ,
nudge_y = nudge_y # from ggrepel
# nudge value for starting point for
# labels (ggrepel)
, ... # in case we need more stuff for ggrepel
)
return.list = structure(list(baseMap = LeG_b,
I_labels = LesGi_dl$leG.labels,
I_points = LesGi_dl$leG.points,
J_labels = LesGj_dl$leG.labels,
J_points = LesGj_dl$leG.points),
class = 'createFactorMapIJ')
return(return.list)
} # End of Function
#
#_____________________________________________________________________
# Change the print function for
# the createFactorMapIJ environment
#
#' Change the print function for createFactorMapIJ
#'
#' Change the print function for createFactorMapIJ
#'
#' @param x a list: output of createFactorMapIJ
#' @param ... everything else for the functions
#' @author Herve Abdi
#' @export
print.createFactorMapIJ <- function (x, ...) {
ndash = 78 # How many dashes for separation lines
cat(rep("-", ndash), sep = "")
cat("\nThe base map and 4 Sub-Maps for Correspondence Analysis \n")
# cat("\n List name: ",deparse(eval(substitute(substitute(x)))),"\n")
cat(rep("-", ndash), sep = "")
cat("\n$baseMap ", "The Base Map to which the subMaps are added")
cat("\n$I_labels ", "I-Set (row) Labels")
cat("\n$I_points ", "I-Set (row) Points")
cat("\n$J_labels ", "J-Set (col) Labels")
cat("\n$J_points ", "J-Set (col) Points")
cat("\n",rep("-", ndash), sep = "")
cat("\n")
invisible(x)
} # end of function print.createFactorMapIJ
#_____________________________________________________________________
#_____________________________________________________________________
#' @title Creates all the partial ggplot2 maps for CA
#' with all standard variants of normalization for factor scores.
#'
#' @description \code{createAllMaps4CA}: uses
#' \code{ggplot2} to
#' 1) create all the partial maps for CA
#' with the different types of normalizations: Asymmetric,
#' Symmetric, True-Barycentric, Biplots, and \code{SPSS}
#' pseudo Biplots.
#' 2)
#' to creates \code{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 \eqn{I} (rows) and the
#'\eqn{J} (column) -sets.
#'
#' @param allNormedFactors,
#' A list with all the
#' factor scores normed
#' typically from \code{createAllNormedFactors}.
#' @param axis1 the column of X used for the horizontal axis
#' of the plot. Default = 1.
#' @param axis2 the column of X used for the vertical axis
#' of the plot. Default = 2.
#' @param title A main title (default is \code{NULL}).
#' @param col.points.i the color of the points/dots
#' for the \eqn{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 = \code{'blueviolet'}.
#' @param alpha.points.i (default = .5), the alpha
#' (transparency) for the points, should be
#' between 1 (opaque) and 0
#' (completely transparent).
#' @param pch.i the character for the points for the \eqn{I}-set.
#' Default is 19 (Circles).
#' @param cex.i size of the dots for the \eqn{I}-set.
#' Default = 2.5
#' @param col.labels.i the color of the labels for
#' the \eqn{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 = \code{'darkorchid'}.
#' @param alpha.labels.i (default = 1), the alpha
#' (transparency) for the labels, should be
#' between 1 (opaque) and 0
#' (completely transparent).
#' @param text.cex.i = 4, font size for labels for the I-set.
#' @param segment.size.i = 0, # size of segment
#' @param font.face.i (Default = \code{'bold'})
#' font for labels for the \eqn{I}-set.
#' @param font.family.i (Default = \code{'sans'})
#' font family for the \eqn{I}-set.
#' @param force.i (Default = 1)
#' How much \code{ggrepel} repels the labels
#' for the \eqn{I}-set.
#' @param col.points.j
#' the color of the points/dots for the \eqn{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 = \code{'darkolivegreen4'}.
#' @param alpha.points.j (Default = .5), the alpha
#' (transparency) for the \eqn{J}-points, should be
#' between 1 (opaque) and 0
#' (completely transparent).
#' @param pch.j the character for the points for the \eqn{J}-set.
#' Default is 18 (Diamonds).
#' @param cex.j size of the dots for the \eqn{J}-set.
#' Default = 2.5
#' @param segment.size.j = 0, # size of segment for \eqn{J}-set
#' @param col.labels.j the color of the labels for
#' the \eqn{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 = \code{'darkolivegreen'}.
#' @param alpha.labels.j (default = 1), the alpha
#' (transparency) for the \eqn{J}-labels, should be
#' between 1 (opaque) and 0
#' (completely transparent).
#' @param text.cex.j (Default = 4)
#' font size for labels for the \eqn{J}-set.
#' @param font.face.j (Default = \code{'bold'}
#' font for the labels for the \eqn{J}-set.
#' @param font.family.j (Default = \code{'sans'})
#' font family for the \eqn{J}-set.
#' @param force.j (Default = 1). How much \code{ggrepel} repels
#' the labels for the \eqn{J}-set.
#' @param col.axes (Default = \code{'darkorchid'})
#' color for the axes.
#' @param alpha.axes
#' (Default = .2) transparency factor for the
#' color of the axes.
#' @param width.axes (Default = 1.1) the width of the axes
#' @param col.background
#' [Default = \code{adjustcolor('lavender', alpha.f = .2)}],
#' The color of the background.
#' @param ... eveythings else for the functions.
#' @return a list with
#' \code{baseMap_S:} The Background (Symmetric)
#' \code{I_labels_S} The labels I-set (Symmetric).
#' \code{I_points_S} The dots I-set (Symmetric).
#' \code{J_labels_S} The labels J-set (Symmetric).
#' \code{J_points_S} The dots J-set(Symmetric).
#' \code{baseMap_A} The Background (Asymmetric)
#' \code{I_labels_A} The labels I-set (Asymmetric).
#'\code{I_points_A} The dots I-set (Asymmetric).
#' \code{J_labels_A} The labels J-set (Asymmetric).
#' \code{J_points_A} The dots J-set (Asymmetric).
#' \code{baseMap_B} The Background (Barycentric).
#' \code{I_labels_B} The labels I-set (Barycentric).
#' \code{I_points_B} The dots I-set (Barycentric).
#' \code{J_labels_B} The labels J-set (Barycentric).
#' \code{J_points_B} The dots J-set (Barycentric).
#; NB class = 'createAllMaps4CA'
#' @details The final maps are built
#' by combining the elementary maps.
#' For example, a map with the \eqn{J}-set being asymmetric
#' and the \eqn{I}-set being Symmetric would be made
#' by creating the \code{Ja_Is} map as
#' \code{Ja_Is <- baseMap_A + J_labels_A + I_labels_S}.
#'
#' Note than, in general, the \code{Asymmetric} is larger than the
#' \code{Symmetric} map which is in turn larger than the
#' \code{Barycentric} map.
#' @section Important_Note:
#' When creating multiple layers graphs,
#' because of the way \code{ggplot2} create graphs,
#' all
#' the matrices/dataframe should all the have
#' the same column names
#' [e.g., \code{colnames()}
#' 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").
#' @export
# @examples \dontrun{}
#' @author Hervé Abdi
#' @seealso createFactorMaps createbaseMap
createAllMaps4CA <- function(allNormedFactors,
# A list with all the
# factor scores normed
# typically from createAllNormedFactors
axis1 = 1, axis2 = 2,
# defaultnames for the graphs
# constraints = NULL,
# list with minx miny maxx maxy
# as obtained, e.g.,
# from minmacHelper from prettyGraphs
title = NULL,
# The I-set
col.points.i = 'blueviolet',
#display.points.i = TRUE,
alpha.points.i = .5,
pch.i = 19, # Character for the dots
# 19 is circle
cex.i = 2.5, # size of the dots
segment.size.i = 0, # size of segment
#display.labels.i = TRUE,
col.labels.i = 'darkorchid4',
alpha.labels.i = 1, # alapha for text
text.cex.i = 4, # font size for labels
font.face.i = 'bold', # font for labels
font.family.i = 'sans' ,
force.i = 1 , # force repel factor for ggrepel
# The J-set
col.points.j = 'darkolivegreen4',
alpha.points.j = .5,
#display.points.j = TRUE,
pch.j = 18, # Character for the dots
# 18 is diamond
cex.j = 2.5, # size of the dots
segment.size.j = 0, # size of segment
#display.labels.j = TRUE,
col.labels.j = 'darkolivegreen',
alpha.labels.j = 1,
text.cex.j = 4, # font size for labels
font.face.j = 'bold', # font for labels
font.family.j = 'sans' ,
# font family for labels
force.j = 1 , # force repel factor for ggrepel
col.axes = 'darkorchid',
# color for the axes
alpha.axes = .2,
# tranparency for the axes
width.axes = 1.1,
# width of the axes
col.background =
adjustcolor('lavender',
alpha.f = .2),
# background color
... # more stuff
){
# Start with symmetric
#
Fi_S <- allNormedFactors$Fi[,c(axis1,axis2)]
Fj_S <- allNormedFactors$Fj[,c(axis1,axis2)]
# constraints_S <- minmaxHelper(Fi_S, Fj_S)
Maps_S <-
createFactorMapIJ(Fi_S,Fj_S,
axis1 = axis1, axis2 = axis2,
constraints = NULL,
# list with minx miny maxx maxy
# as obtained, e.g.,
# from minmacHelper from prettyGraphs
title = title,
# The I-set
col.points.i = col.points.i,
alpha.points.i = alpha.points.i,
#display.points.i = TRUE,
pch.i = pch.i, # Character for the dots
cex.i = cex.i, # size of the dots
#display.labels.i = TRUE,
col.labels.i = col.labels.i,
alpha.labels.i = alpha.labels.i,
text.cex.i = text.cex.i, # font size for labels
font.face.i = font.face.i , # font for labels
font.family.i = font.family.i,
# The J-set
col.points.j = col.points.j,
alpha.points.j = alpha.points.j,
#display.points.j = TRUE,
pch.j = pch.j, # Character for the dots
cex.j = cex.j, # size of the dots
#display.labels.j = TRUE,
col.labels.j = col.labels.j,
alpha.labels.j = alpha.labels.j,
text.cex.j = text.cex.j, # font size for labels
font.face.j = font.face.j, # font for labels
font.family.j = font.family.j ,
# font family for labels
col.axes = col.axes,
# color for the axes
alpha.axes = alpha.axes,
# tranparency for the axes
width.axes = width.axes,
# width of the axes
col.background = col.background ,
# background color
... # more stuff
)
# Asymetric Maps
#
Fi_A <- allNormedFactors$Fi_A[,c(axis1,axis2)]
Fj_A <- allNormedFactors$Fj_A[,c(axis1,axis2)]
# constraints_S <- minmaxHelper(Fi_S, Fj_S)
Maps_A <-
createFactorMapIJ(Fi_A,Fj_A,
axis1 = axis1, axis2 = axis2,
constraints = NULL,
# list with minx miny maxx maxy
# as obtained, e.g.,
# from minmacHelper from prettyGraphs
title = title,
# The I-set
col.points.i = col.points.i,
alpha.points.i = alpha.points.i,
#display.points.i = TRUE,
pch.i = pch.i, # Character for the dots
cex.i = cex.i, # size of the dots
#display.labels.i = TRUE,
col.labels.i = col.labels.i,
alpha.labels.i = alpha.labels.i ,
text.cex.i = text.cex.i, # font size for labels
font.face.i = font.face.i , # font for labels
font.family.i = font.family.i,
# The J-set
col.points.j = col.points.j,
alpha.points.j = alpha.points.j,
#display.points.j = TRUE,
pch.j = pch.j, # Character for the dots
cex.j = cex.j, # size of the dots
#display.labels.j = TRUE,
col.labels.j = col.labels.j,
alpha.labels.j = alpha.labels.j,
text.cex.j = text.cex.j, # font size for labels
font.face.j = font.face.j, # font for labels
font.family.j = font.family.j ,
# font family for labels
col.axes = col.axes,
# color for the axes
alpha.axes = alpha.axes,
# tranparency for the axes
width.axes = width.axes,
# width of the axes
col.background = col.background ,
# background color
... # more stuff
)
# True Barycentric Maps
#
Fi_B <- allNormedFactors$Fi_B[,c(axis1,axis2)]
Fj_B <- allNormedFactors$Fj_B[,c(axis1,axis2)]
# constraints_S <- minmaxHelper(Fi_S, Fj_S)
Maps_B <-
createFactorMapIJ(Fi_B,Fj_B,
axis1 = axis1, axis2 = axis2,
constraints = NULL,
# list with minx miny maxx maxy
# as obtained, e.g.,
# from minmacHelper from prettyGraphs
title = title,
# The I-set
col.points.i = col.points.i,
alpha.points.i = alpha.points.i,
#display.points.i = TRUE,
pch.i = pch.i, # Character for the dots
cex.i = cex.i, # size of the dots
#display.labels.i = TRUE,
col.labels.i = col.labels.i,
alpha.labels.i = alpha.labels.i,
text.cex.i = text.cex.i, # font size for labels
font.face.i = font.face.i , # font for labels
font.family.i = font.family.i,
# The J-set
col.points.j = col.points.j,
alpha.points.j = alpha.points.j,
#display.points.j = TRUE,
pch.j = pch.j, # Character for the dots
cex.j = cex.j, # size of the dots
#display.labels.j = TRUE,
col.labels.j = col.labels.j,
alpha.labels.j = alpha.labels.j,
text.cex.j = text.cex.j, # font size for labels
font.face.j = font.face.j, # font for labels
font.family.j = font.family.j ,
# font family for labels
col.axes = col.axes,
# color for the axes
alpha.axes = alpha.axes,
# tranparency for the axes
width.axes = width.axes,
# width of the axes
col.background = col.background ,
# background color
... # more stuff
)
return.list = structure(list(baseMap_S = Maps_S$baseMap,
I_labels_S = Maps_S$I_labels,
I_points_S = Maps_S$I_points,
J_labels_S = Maps_S$J_labels,
J_points_S = Maps_S$J_points,
baseMap_A = Maps_A$baseMap,
I_labels_A = Maps_A$I_labels,
I_points_A = Maps_A$I_points,
J_labels_A = Maps_A$J_labels,
J_points_A = Maps_A$J_points,
baseMap_B = Maps_B$baseMap,
I_labels_B = Maps_B$I_labels,
I_points_B = Maps_B$I_points,
J_labels_B = Maps_B$J_labels,
J_points_B = Maps_B$J_points
),
class = 'createAllMaps4CA')
return(return.list)
}
#_____________________________________________________________________
# Change the print function for
# the createAllMaps4CA environment
#
#' Change the print function for createAllMaps4CA
#'
#' Change the print function for createAllMaps4CA
#'
#' @param x a list: output of createAllMaps4CA
#' @param ... everything else for the functions
#' @author Herve Abdi
#' @export
print.createAllMaps4CA <- function (x, ...) {
ndash = 78 # How many dashes for separation lines
cat(rep("-", ndash), sep = "")
cat("\nBasemaps and Point and Labels maps for Correspondence Analysis ")
cat("\nThree Normalizations: Symmetric, Asymmetric, and True Barycentric ")
cat("\nOne Mais is Basemap + dots and / or Labels \n ")
# cat("\n List name: ",deparse(eval(substitute(substitute(x)))),"\n")
cat(rep("-", ndash), sep = "")
cat("\n Symmetric Maps (Inertia = Lambda) \n")
cat(rep("-", ndash), sep = "")
cat("\n$baseMap_S ", "The Base Map to which the subMaps are added")
cat("\n$I_labels_S ", "I-Set (row) Labels")
cat("\n$I_points_S ", "I-Set (row) Points")
cat("\n$J_labels_S ", "J-Set (col) Labels")
cat("\n$J_points_S ", "J-Set (col) Points")
cat("\n",rep("-", ndash), sep = "")
cat("\n Asymmetric Maps (Inertia = Unity) \n")
cat(rep("-", ndash), sep = "")
cat("\n$baseMap_A ", "The Base Map to which the subMaps are added")
cat("\n$I_labels_A ", "I-Set (row) Labels")
cat("\n$I_points_A ", "I-Set (row) Points")
cat("\n$J_labels_A ", "J-Set (col) Labels")
cat("\n$J_points_A ", "J-Set (col) Points")
cat("\n",rep("-", ndash), sep = "")
cat("\n True Barycentric Maps (Inertia = Lambda^2) \n")
cat(rep("-", ndash), sep = "")
cat("\n$baseMap_B ", "The Base Map to which the subMaps are added")
cat("\n$I_labels_B ", "I-Set (row) Labels")
cat("\n$I_points_B ", "I-Set (row) Points")
cat("\n$J_labels_B ", "J-Set (col) Labels")
cat("\n$J_points_B ", "J-Set (col) Points")
cat("\n",rep("-", ndash), sep = "")
cat("\n",rep("-", ndash), sep = "")
cat("\n")
invisible(x)
} # end of function print.createAllMaps4CA
#_____________________________________________________________________
HerveAbdi/PTCA4CATA documentation built on July 17, 2022, 5:41 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions createAllMaps4CA createFactorMapIJ map4DotsAndLabels print.createFactorMap createFactorMap createBaseMap
Documented in createAllMaps4CA createBaseMap createFactorMap createFactorMapIJ map4DotsAndLabels print.createFactorMap
# Preamble ----
#********************************************************************
#_____________________________________________________________________
# function for creating Factor Based Map
# createBaseMap
# createFactorMap
# map4DotsAndLabels
#
# Revision October/21/2017. in createFactorMap
# fix problem with axis different from 1 and 2
#
#_____________________________________________________________________
# function: createBaseMap
# createBaseMap ----
#_____________________________________________________________________
#' create a base map for CA type graphs with ggplot2
#'
#' \code{createBaseMap}: Create a ggplot2 basemap for CA type graphs.
#' The final maps are created by using overlays.
#' A map CA is created with first the baseMap and
#' then adding a text/dot map.
#' @seealso \code{\link{createFactorMapIJ}}
#' @param data the factor scores to plot
#' @param constraints a list with minx miny maxx maxy
#' typically obtained from \code{prettyGraphs::minmaxHelper()}.
#' If \code{NULL}
#' (default) it is computed with the function
#' \code{prettyGraphs::minmaxHelper()}.
#' @param col.axes color for the axes, default is
#' \code{'darkorchid'}.
#' @param alpha.axes alpha parametere (transparency)
#' for the axes, default is .2.
#' @param width.axes the width of the axes, default is 1.1.
#' @param col.background the color theme of the background,
#' default is \code{adjustcolor('lavender', alpha.f = .2)}.
#' @param title a main title, default is \code{NULL} (no title)
#' @return a basemap
#' @import prettyGraphs ggplot2 grDevices
#' @export
#' @author Hervé Abdi
#' @section Important_Note: When creating multiple layers graphs,
#' because of the way \code{ggplot2} create graphs, all the
#' the matrices/dataframe should all the have the same column names
#' [e.g., \code{colnames()} equal to
#' \code{c("Dimension 1", "Dimension 2")}].
#' When it is not the case, some strange and cryptic
#' error may be produced
#' (e.g., \code{"cannot find Dimension"}).
#' @examples \dontrun{
#' aBaseMap <- createBaseMap(Fi)
#' # with Fi being a map of factor scores
#' }
createBaseMap <- function(data,
constraints = NULL,
col.axes = 'darkorchid',
alpha.axes = .2,
width.axes = 1.1,
col.background =
adjustcolor('lavender',
alpha.f = .2),
title = NULL){
if (is.null(col.background)){col.background = 'transparent'}
data <- as.data.frame(data)
if (is.null(constraints)) {
# lapply(prettyGraphs::minmaxHelper(Fj[,3:4]),'*',1.1)
constraints <- lapply(prettyGraphs::minmaxHelper(data),'*',1.1)
}
V1 = as.name(colnames(data)[1])
V2 = as.name(colnames(data)[2])
# Create a Background Map
LeG_b <- ggplot(data = data,
# aes(data[,1],data[2])
aes_string(V1, V2)
) +
coord_fixed(ratio = 1)
LeG_b = LeG_b +
xlim(constraints$minx,constraints$maxx) +
ylim(constraints$miny,constraints$maxy)
LeG_b <- LeG_b + geom_hline(yintercept = 0, size = width.axes,
color = col.axes,alpha = alpha.axes) +
geom_vline(xintercept = 0, size = width.axes ,
color = col.axes,alpha = alpha.axes) +
theme(panel.background = element_rect(fill = col.background,
color = col.axes))
if (!is.null(title))LeG_b <- LeG_b + ggtitle(title)
return(LeG_b)
}
# End of function createBaseMap
#_____________________________________________________________________
# function: createFactorMap
#_____________________________________________________________________
# createFactorMap ----
# create the base plot for factor type plots
# gives a baseMap and one map for dots and one map for labels
#_____________________________________________________________________
#' @title create the base plot maps for CA type
#' graphs with \code{ggplot2}.
#'
#' @description \code{createFactorMap}:
#' Creates the \code{ggplot2} basic factor maps for CA type graphs.
#' The final maps are created by using overlays on top of the base map.
#'
#' A map for CA is created with the baseMap to which
#' is added text/dot map.
#' \code{createFactorMap} calls the functions \code{map4DotsAndLabels}
#' and \code{createBaseMap}.
#'
#' @seealso \code{\link{map4DotsAndLabels}}
#' \code{\link{createBaseMap}}
#' .
#' @param X the factor scores to plot.
#' @param axis1 the column of X used for the horizontal axis
#' of the plot. Default = 1.
#' @param axis2 the column of X used for the vertical axis
#' of the plot. Default = 2.
#' @param constraints a list with \code{minx miny maxx maxy},
#' typically obtained from \code{ExPosition}. If \code{NULL}
#' (default) it is computed with the function
#' \code{prettyGraphs::minmaxHelper()}.
#' @param title A title for the graph. Default is \code{NULL}.
#' @param col.points the color of the points/dots.
#' 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 = \code{'blueviolet'}.
#' @param alpha.points (default = .5), the alpha
#' (transparency) for the points, should be
#' between 1 (opaque) and 0
#' (completely transparent).
#' @param display.points if \code{TRUE} (Default)
#' create the map for the points.
#' @param pch the character for the points,
#' Default is 19 (circles).
#' @param cex size of the dots. Default = 2.5
#' @param display.labels if \code{TRUE} (Default),
#' create the
#' map for the labels.
#' @param col.labels the color of the labels
#' 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 = \code{'darkorchid'}.
#' @param alpha.labels (default = 1), the alpha
#' (transparency) for the points, should be
#' between 1 (no transparency) and 0
#' (completely transparent).
#' @param text.cex = 4, font size for labels.
#' @param font.face (Default = \code{'bold'}) font for labels.
#' @param font.family (Default = \code{'sans'})
#' font family for labels.
#' @param col.axes color for the axes, default is
#' \code{'darkorchid'}.
#' @param alpha.axes alpha parameter (transparency)
#' for the axes, default is .2.
#' @param width.axes the width of the axes, default is 1.1.
#' @param col.background the color theme of the background,
#' default is \code{adjustcolor('lavender', alpha.f = .2)}.
#' @param force \code{(default = 1)}.
#' How much \code{ggrepel} repels the label
#' @param segment.size \code{(default = 0)}
#' size of segment line for \code{ggrpel}.
#' @param ... stuff to be passed to other functions.
#' @return a list with 6 elements:
#' \enumerate{
#' \item \code{zeMap}: The Complete Map (background Dots and Labels);
#' \item \code{zeMap_background}: The Background;
#' \item \code{zeMap_dots:}: The dots;
#' \item \code{zeMap_text:}: The Labels;
#' \item \code{factorScores:}: The factor scores; and
#' \item \code{constraints:}: The list of the contraints'
#' }
#; NB class = \code{'createFactorMap'}.
#' @section Important_Note: When creating multiple layers graphs,
#' because of the way \code{ggplot2} create graphs, all
#' the matrices/dataframe should all the have the same column names
#' [e.g., \code{colnames()} equal to
#' \code{c("Dimension 1", "Dimension 2")}].
#' When it is not the case, some strange and cryptic
#' error may be produced
#' (e.g., \code{"cannot find Dimension"}).
#' @import prettyGraphs grDevices
#' @export
# @examples \dontrun{}
#' @author Hervé Abdi
createFactorMap <- function(X,
axis1 = 1, axis2 = 2,
constraints = NULL,
# list with minx miny maxx maxy
# as obtained, e.g.,
# from minmacHelper from prettyGraphs
title = NULL,
col.points = 'blueviolet',
alpha.points = .5,
display.points = TRUE,
pch = 19, # Character for the dots
cex = 2.5, # size of the dots
display.labels = TRUE,
col.labels = 'darkorchid4',
alpha.labels = 1,
text.cex = 4, # font size for labels
font.face = 'bold', # font for labels
font.family = 'sans' ,
# font family for labels
col.axes = 'darkorchid',
# color for the axes
alpha.axes = .2,
# tranparency for the axes
width.axes = 1.1,
# width of the axes
col.background =
adjustcolor('lavender',
alpha.f = .2),
force = 1, # for ggrepel
segment.size = 0, # size of segment line
# background color
... # more stuff
){ #col.labels <- ggplot2::alpha(col.labels, alpha = alpha.labels)
#col.points <- ggplot2::alpha(col.points, alpha = alpha.points)
#
if (is.null(title)){title = ''}
#
# give a name to the Dimension of Fi is there is none
if (is.null(colnames(X))){
colnames(X) <- paste0('Dimension ',1:ncol(X))
}
# G = as.data.frame(X[,c(axis1,axis2)])
G = as.data.frame(X)
#V1 = as.name(colnames(G)[1])
#V2 = as.name(colnames(G)[2])
# NB default uses minmaxHelper from prettyPlots
if (is.null(constraints)){
constraints <-
lapply(prettyGraphs::minmaxHelper(G[,c(axis1,axis2)]),'*',1.1)
}
#
#___________________________________________________________________
# NB geom_text_repel is from ggrepel
LeG_b <- createBaseMap(data = G[,c(axis1,axis2)],
constraints = constraints,
col.axes = col.axes, # 'darkorchid',
alpha.axes = alpha.axes,
width.axes = width.axes,
col.background = col.background,
title = title)
LesG_dl <- map4DotsAndLabels(
data = G[,c(axis1,axis2)],
axis1 = 1,
axis2 = 2,
display.points = display.points,
col.points = col.points,
alpha.points = alpha.points,
pch = pch,
# Character for the points
cex = cex,
# size of the points
display.labels = display.labels,
col.labels = col.labels,
alpha.labels = alpha.labels,
text.cex = text.cex,
# font size for labels
font.face = font.face, #'bold',
# font for labels
font.family = font.family ,'sans',
# font family for labels
# below are ggrepel values
force = force, # labels' repulsion for ggrepel
segment.size = segment.size,
# segment width for ggrepel
nudge_x = 0,
nudge_y = 0 # from ggrepel
# nudge value for starting point for
# labels (ggrepel)
, ... # in case we need more stuff for ggrepel
)
LeG = LeG_b
if (display.points){LeG = LeG + LesG_dl$leG.points}
if (display.labels){LeG = LeG + LesG_dl$leG.labels}
return.list <- structure(list(zeMap = LeG,
zeMap_background = LeG_b,
zeMap_dots = LesG_dl$leG.points,
zeMap_text = LesG_dl$leG.labels,
factorScores = G, constraints = constraints),
class = 'createFactorMap')
return(return.list)
#
} # End of Function
#_____________________________________________________________________
#' Change the print function for \code{createFactorMap}
#'
#' Change the print function for objsects of the
#' class \code{createFactorMap}
#'
#' @param x a list: output of \code{createFactorMap}
#' @param ... everything else for the functions
#' @author Herve Abdi
#' @export
print.createFactorMap <- function(x, ...) {
ndash = 78 # How many dashes for separation lines
cat(rep("-", ndash), sep = "")
cat("\nBasic Factor Maps (with ggplot2) \n")
# cat("\n List name: ",deparse(eval(substitute(substitute(x)))),"\n")
cat(rep("-", ndash), sep = "")
cat("\n$zeMap ", "A standard map with background, points, and Labels")
cat("\n$zeMap_background ", "The background map")
cat("\n$zeMap_dots ", "The points map")
cat("\n$zeMap_text ", "The labels map")
cat("\n$factorScores ", "The factor scores (coordinates)")
cat("\n$constraints ", "map constraints (a list with minx miny maxx maxy)")
cat("\n",rep("-", ndash), sep = "")
cat("\n")
invisible(x)
} # end of function print.createNormedFactors
#_____________________________________________________________________
#_____________________________________________________________________
# function: map4DotsAndLabels ----
#_____________________________________________________________________
#' Create \code{ggplot2} factorial maps for dots and labels.
#'NB needs a base map to work correctly
#'
#' \code{map4DotsAndLabels}:
#' Creates \code{ggplot2} factorial map for dots and labels.
#'NB: needs a base map to work correctly.
#' create the base plot maps for CA type graphs with \code{ggplot2}
#'
#' @param data the factor scores to plot
#' @param axis1 the column of X used for the horizontal axis
#' of the plot. \code{Default 1}.
#' @param axis2 the column of \code{X} used for the vertical axis
#' of the plot. \code{Default 2}.
#' @param display.points if \code{TRUE} (Default)
#' create the map for the points.
#' @param col.points the color of the points/dots.
#' Can be one color or a vector of colors. If a vector it needs
#' to have exactly the number of items to be plotted.
#' \code{Default = 'blueviolet'}.
#' @param alpha.points \code{(default = .5)}, the alpha
#' (transparency) for the points, should be
#' between 1 (no transparency) and 0
#' (completely transparent).
#' @param pch the character for the points,
#' Default is 19 (Circles).
#' @param cex size of the dots. Default = 2.5
#' @param display.labels if \code{TRUE} (default), create the
#' map for the labels.
#' @param col.labels the color of the labels
#' 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 = \code{'darkorchid'}.
#' @param alpha.labels (default = 1), the alpha
#' (transparency) for the labels, should be
#' between 1 (no transparency) and 0
#' (completely transparent).
#' @param force = 1. How much \code{ggrepel} repels the labels.
#' @param segment.size = 0,
#' size of segment line for \code{ggrpel}.
#' @param text.cex = 4, font size for labels.
#' @param font.face (default = \code{'bold'}) font for labels.
#' @param font.family (default = \code{'sans'}),
#' font family for labels.
#' @param nudge_x (default = 0). From \code{ggrepel},
#' nudge value for starting point for
#' labels: x dimension.
#' @param nudge_y (default = 0). From \code{ggrepel},
#' nudge value for starting point for
#' labels: y dimension.
#' @param alpha.point (default = .5), the alpha
#' (transparency) for the points, should be
#' between 1 (no transparency) and 0
#' (completely transparent).
#' @param ... everything else to pass to the functions
#' @return a list with 6-elements:
#' \enumerate{
#' \item \code{zeMap}: The Complete Map (background Dots and Labels);
#' \item \code{zeMap_background}: The Background map;
#' \item \code{zeMap_dots:} The dots;
#' \item \code{zeMap_text:} The Labels;
#' \item \code{factorScores:} The factor scores; and
#' \item \code{constraints:} The list of the contraints
#' (could be used to generate other graphs
#' with the same scaling factors).
#' }
#; NB class = 'createFactorMap'
#' @section Important_Note: When creating multiple layers graphs,
#' because of the way \code{ggplot2} create graphs, all
#' the matrices/dataframe should all the have the same column names
#' [e.g., \code{colnames()} equal to
#' \code{c("Dimension 1", "Dimension 2")}].
#' When it is not the case, some strange and cryptic
#' error may be produced
#' (e.g., \code{"cannot find Dimension"}).
#' @import ggplot2 ggrepel
#' @export
#' @author Herve Abdi
#' @rdname map4DotsAndLabels
#' @seealso \code{\link{createFactorMap}} \code{\link{createBaseMap}}
map4DotsAndLabels <- function(data,
axis1 = 1, axis2 = 2,
display.points = TRUE,
col.points = 'blueviolet',
alpha.points = .5,
pch = 19, # Character for the points
cex = 2.5, # size of the points
display.labels = TRUE,
col.labels = 'darkorchid4',
alpha.labels = 1,
force = 1,
segment.size = 0,
# segment width for ggrepel
text.cex = 4,
# font size for labels
font.face = 'bold',
# font for labels
font.family = 'sans',
# font family for labels
nudge_x = 0, nudge_y = 0, # from ggrepel
# nudge value for starting point for
# labels
... # for ggrepel in case
){# function map4DotsAndLabels start here
data <- as.data.frame(data) # make sure that we a df
V1 = as.name(colnames(data)[1])
V2 = as.name(colnames(data)[2])
# Create the Dot-map
LeG_dot = NULL
if (display.points){
LeG_dot =
# Next describe the points
ggplot2::geom_point(
data = data,
aes_string(V1, V2),
shape = pch,
size = cex,
color = col.points,
alpha = alpha.points# ,alpha = .5
)
}
# Create the text-map
LeG_text = NULL
if (display.labels){
LeG_text = # The text
ggrepel::geom_text_repel(
label = rownames(data),
data = data,
aes_string(V1, V2),
#aes(G[,1],G[,2]),
segment.size = segment.size,
size = text.cex,
fontface = font.face,
family = font.family,
color = col.labels,
alpha = alpha.labels,
nudge_x = nudge_x,
nudge_y = nudge_y
)
}
return(list(leG.points = LeG_dot, leG.labels = LeG_text))
} # End of function.
# function map4DotsAndLabels ends here
#_____________________________________________________________________
#_____________________________________________________________________
#_____________________________________________________________________
# function: createFactorMapIJ
#_____________________________________________________________________
#' Create
#' ggplot2 factorial maps for CA-type of maps dots and labels.
#'
#' \code{createFactorMapIJ}: Creates
#' \code{ggplot2} factorial maps for dots and labels.
#'NB needs a base map to work correctly.
#'
#' @param Fi the \eqn{I}-set factor scores to plot
#' @param Fj the \eqn{J}-set factor scores to plot
#' @param axis1 the column of X used for the horizontal axis
#' of the plot. Default 1.
#' @param axis2 the column of X used for the vertical axis
#' of the plot. Default 2.
#' @param constraints a list with minx miny maxx maxy
#' typically obtained from \code{prettyGraphs::minmaxHelper()}.
#' If \code{NULL}
#' (default) it is computed with the function
#' \code{prettyGraphs::minmaxHelper()}.
#' @param title a title for the plots.
#' @param col.points.i the color of the points/dots for the \eqn{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 = \code{'blueviolet'}.
#' @param alpha.points.i (default = .5), the alpha
#' (transparency) for the points, should be
#' between 1 (no transparency) and 0
#' (completely transparent).
#' @param pch.i the character for the points for the \eqn{I}-set.
#' Default is 19 (Circles).
#' @param cex.i size of the dots for the \eqn{I}-set. Default = 2.5
#' @param col.labels.i the color of the labels for
#' the \eqn{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 = \code{'darkorchid'}.
#' @param alpha.labels.i (default = 1), the alpha
#' (transparency) for the \eqn{I}-labels, should be
#' between 1 (no transparency) and 0
#' (completely transparent).
#' @param text.cex.i = 4, font size for labels for the I-set.
#' @param segment.size.i = 0, # size of segment
#' @param font.face.i (Default = \code{'bold'},
#' font for labels for the \eqn{I}-set.
#' @param font.family.i (Default = \code{'sans'})
#' font family for the \eqn{I}-set.
#' @param force.i (Default = 1). How much ggrepel repels the labels
#' for the \eqn{I}-set.
#' @param col.points.j the color of the points/dots
#' for the \eqn{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 = \code{'darkolivegreen4'}.
#' @param alpha.points.j (default = .5), the alpha
#' (transparency) for the points, should be
#' between 1 (no transparency) and 0
#' (completely transparent).
#' @param pch.j the character for the points for the \code{J}-set.
#' Default is 18 (Diamonds).
#' @param cex.j size of the dots for the \eqn{J}-set. Default = 2.5
#' @param segment.size.j = 0, # size of segment for \eqn{J}-set
#' @param col.labels.j the color of the labels for
#' the \eqn{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 = \code{'darkolivegreen'}.
#' @param alpha.labels.j (default = 1), the alpha
#' (transparency) for the \eqn{J}-labels, should be
#' between 1 (no transparency) and 0
#' (completely transparent).
#' @param text.cex.j (Default = 4), font size for labels for the J-set.
#' @param font.face.j (Default = \code{'bold'}),
#' font for labels for the \eqn{J}-set.
#' @param font.family.j (Default = \code{'sans'})
#' font family for the \eqn{J}-set.
#' @param force.j = 1. How much ggrepel repels
#' the labels for the \eqn{J}-set.
#' @param col.axes (Default = \code{'darkorchid'})
#' color for the axes
#' @param alpha.axes (Default = .2) transoarency factors for the
#' color of the axes.
#' @param width.axes (Default = 1.1) the width of the axes
#' @param col.background [Default =
#' \code{adjustcolor('lavender', alpha.f = .2)}]
#' The color of the background.
#' @param nudge_x = 0. From \code{ggrepel},
#' nudge value for starting point for
#' labels: x dimension.
#' @param nudge_y = 0. From \code{ggrepel},
#' nudge value for starting point for
#' labels: y dimension.
#' @param ... everything else for the functions
#' @return a list with
#' 1) \code{zeMap:} The Complete Map (background Dots and Labels);
#' 2) \code{zeMap_background:} The background;
#' 3) \code{zeMap_dots:} The dots;
#' 4) \code{zeMap_text:} The labels;
#' 5) \code{factorScores}: The factor scores; and
#' 6) \code{constraints:} The list of the contraints.
#; NB class = 'createFactorMap'
#' @section Important_Note: When creating multiple layers graphs,
#' because of the way \code{ggplot2} creates graphs, all the
#' the matrices/dataframe should all the have the same column names
#' [e.g., \code{colnames()} equal to c("Dimension 1", "Dimension 2")].
#' When it is not the case, some strange and cryptic
#' error may be produced
#' (e.g., "cannot find Dimension").
#' @import prettyGraphs
#' @export
# @examples \dontrun{}
#' @author Herve Abdi
#' @seealso createFactorMaps createbaseMap
# Function
# createFactorMapIJ
# createFactorMapIJ
# create the base plot for factor type plots
# give a baseMap and one map for dots and one map for labels
#
createFactorMapIJ <- function(Fi,Fj,
axis1 = 1, axis2 = 2,
constraints = NULL,
# list with minx miny maxx maxy
# as obtained, e.g.,
# from minmacHelper from prettyGraphs
title = NULL,
# The I-set
col.points.i = 'blueviolet',
alpha.points.i = .5,
# display.points.i = TRUE,
pch.i = 19, # Character for the dots
cex.i = 2.5, # size of the dots
segment.size.i = 0, # size of segment
# display.labels.i = TRUE,
col.labels.i = 'darkorchid4',
alpha.labels.i = 1,
text.cex.i = 4, # font size for labels
font.face.i = 'bold', # font for labels
font.family.i = 'sans' ,
force.i = 1 , # force repel factor for ggrepel
# The J-set
col.points.j = 'darkolivegreen4',
#display.points.j = TRUE,
alpha.points.j = .5,
pch.j = 18, # Character for the dots
cex.j = 2.5, # size of the dots
segment.size.j = 0, # size of segment
#display.labels.j = TRUE,
col.labels.j = 'darkolivegreen',
alpha.labels.j = .5,
text.cex.j = 4, # font size for labels
font.face.j = 'bold', # font for labels
font.family.j = 'sans' ,
force.j = 1 , # force repel factor for ggrepel
# font family for labels
col.axes = 'darkorchid',
# color for the axes
alpha.axes = .2,
# transparency for the axes
width.axes = 1.1,
# width of the axes
col.background =
adjustcolor('lavender',
alpha.f = .2),
# background color
nudge_x = 0,
nudge_y = 0,
... # more stuff
){
#
if (is.null(title)){title = ''}
# Use ggplot from ggplot2
#
Fi <- as.data.frame( Fi[,c(axis1,axis2)])
Fj <- as.data.frame( Fj[,c(axis1,axis2)])
# give a name to the Dimension of Fi is there is none
if (is.null(colnames(Fi))){
colnames(Fi) <- paste0('Dimension ',1:ncol(Fi))
colnames(Fj) <- paste0('Dimension ',1:ncol(Fj))
}
# G = as.data.frame(Fi[,c(axis1,axis2)])
#V1 = as.name(colnames(G)[1])
#V2 = as.name(colnames(G)[2])
# NB default uses minmaxHelper from prettyPlots
if (is.null(constraints)){
constraints <-
lapply(prettyGraphs::minmaxHelper(Fi,Fj),'*',1.1)
}
#___________________________________________________________________
# First the basemao
LeG_b <- createBaseMap(data = rbind(Fi,Fj),
constraints = constraints,
col.axes = col.axes, # 'darkorchid',
alpha.axes = alpha.axes,
width.axes = width.axes,
col.background = col.background,
title = title)
# dots and labels map
LesGi_dl <- map4DotsAndLabels(
data = Fi,
axis1 = 1,
axis2 = 2,
# display.points = TRUE,
col.points = col.points.i,
alpha.points.i = alpha.points.i,
pch = pch.i,
# Character for the points
cex = cex.i,
# size of the points
#display.labels = display.labels,
col.labels = col.labels.i,
alpha.labels.i = alpha.labels.i,
text.cex = text.cex.i,
# font size for labels
font.face = font.face.i, #'bold',
# font for labels
font.family = font.family.i , # 'sans',
# font family for labels
# below are ggrepel values
force = force.i, # labels' repulsion for ggrepel
segment.size = segment.size.i,
# segment width for ggrepel
nudge_x = nudge_x ,
nudge_y = nudge_y # from ggrepel
# nudge value for starting point for
# labels (ggrepel)
, ... # in case we need more stuff for ggrepel
)
LesGj_dl <- map4DotsAndLabels(
data = Fj,
axis1 = 1,
axis2 = 2,
#display.points = display.points,
col.points = col.points.j,
alpha.points.j = alpha.points.j,
pch = pch.j,
# Character for the points
cex = cex.j,
# size of the points
#display.labels = display.labels,
col.labels = col.labels.j,
alpha.points.j = alpha.points.j,
text.cex = text.cex.j,
# font size for labels
font.face = font.face.j, #'bold',
# font for labels
font.family = font.family.j ,# 'sans',
# font family for labels
# below are ggrepel values
force = force.j, # labels' repulsion for ggrepel
segment.size = segment.size.j,
# segment width for ggrepel
nudge_x = nudge_x ,
nudge_y = nudge_y # from ggrepel
# nudge value for starting point for
# labels (ggrepel)
, ... # in case we need more stuff for ggrepel
)
return.list = structure(list(baseMap = LeG_b,
I_labels = LesGi_dl$leG.labels,
I_points = LesGi_dl$leG.points,
J_labels = LesGj_dl$leG.labels,
J_points = LesGj_dl$leG.points),
class = 'createFactorMapIJ')
return(return.list)
} # End of Function
#
#_____________________________________________________________________
# Change the print function for
# the createFactorMapIJ environment
#
#' Change the print function for createFactorMapIJ
#'
#' Change the print function for createFactorMapIJ
#'
#' @param x a list: output of createFactorMapIJ
#' @param ... everything else for the functions
#' @author Herve Abdi
#' @export
print.createFactorMapIJ <- function (x, ...) {
ndash = 78 # How many dashes for separation lines
cat(rep("-", ndash), sep = "")
cat("\nThe base map and 4 Sub-Maps for Correspondence Analysis \n")
# cat("\n List name: ",deparse(eval(substitute(substitute(x)))),"\n")
cat(rep("-", ndash), sep = "")
cat("\n$baseMap ", "The Base Map to which the subMaps are added")
cat("\n$I_labels ", "I-Set (row) Labels")
cat("\n$I_points ", "I-Set (row) Points")
cat("\n$J_labels ", "J-Set (col) Labels")
cat("\n$J_points ", "J-Set (col) Points")
cat("\n",rep("-", ndash), sep = "")
cat("\n")
invisible(x)
} # end of function print.createFactorMapIJ
#_____________________________________________________________________
#_____________________________________________________________________
#' @title Creates all the partial ggplot2 maps for CA
#' with all standard variants of normalization for factor scores.
#'
#' @description \code{createAllMaps4CA}: uses
#' \code{ggplot2} to
#' 1) create all the partial maps for CA
#' with the different types of normalizations: Asymmetric,
#' Symmetric, True-Barycentric, Biplots, and \code{SPSS}
#' pseudo Biplots.
#' 2)
#' to creates \code{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 \eqn{I} (rows) and the
#'\eqn{J} (column) -sets.
#'
#' @param allNormedFactors,
#' A list with all the
#' factor scores normed
#' typically from \code{createAllNormedFactors}.
#' @param axis1 the column of X used for the horizontal axis
#' of the plot. Default = 1.
#' @param axis2 the column of X used for the vertical axis
#' of the plot. Default = 2.
#' @param title A main title (default is \code{NULL}).
#' @param col.points.i the color of the points/dots
#' for the \eqn{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 = \code{'blueviolet'}.
#' @param alpha.points.i (default = .5), the alpha
#' (transparency) for the points, should be
#' between 1 (opaque) and 0
#' (completely transparent).
#' @param pch.i the character for the points for the \eqn{I}-set.
#' Default is 19 (Circles).
#' @param cex.i size of the dots for the \eqn{I}-set.
#' Default = 2.5
#' @param col.labels.i the color of the labels for
#' the \eqn{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 = \code{'darkorchid'}.
#' @param alpha.labels.i (default = 1), the alpha
#' (transparency) for the labels, should be
#' between 1 (opaque) and 0
#' (completely transparent).
#' @param text.cex.i = 4, font size for labels for the I-set.
#' @param segment.size.i = 0, # size of segment
#' @param font.face.i (Default = \code{'bold'})
#' font for labels for the \eqn{I}-set.
#' @param font.family.i (Default = \code{'sans'})
#' font family for the \eqn{I}-set.
#' @param force.i (Default = 1)
#' How much \code{ggrepel} repels the labels
#' for the \eqn{I}-set.
#' @param col.points.j
#' the color of the points/dots for the \eqn{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 = \code{'darkolivegreen4'}.
#' @param alpha.points.j (Default = .5), the alpha
#' (transparency) for the \eqn{J}-points, should be
#' between 1 (opaque) and 0
#' (completely transparent).
#' @param pch.j the character for the points for the \eqn{J}-set.
#' Default is 18 (Diamonds).
#' @param cex.j size of the dots for the \eqn{J}-set.
#' Default = 2.5
#' @param segment.size.j = 0, # size of segment for \eqn{J}-set
#' @param col.labels.j the color of the labels for
#' the \eqn{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 = \code{'darkolivegreen'}.
#' @param alpha.labels.j (default = 1), the alpha
#' (transparency) for the \eqn{J}-labels, should be
#' between 1 (opaque) and 0
#' (completely transparent).
#' @param text.cex.j (Default = 4)
#' font size for labels for the \eqn{J}-set.
#' @param font.face.j (Default = \code{'bold'}
#' font for the labels for the \eqn{J}-set.
#' @param font.family.j (Default = \code{'sans'})
#' font family for the \eqn{J}-set.
#' @param force.j (Default = 1). How much \code{ggrepel} repels
#' the labels for the \eqn{J}-set.
#' @param col.axes (Default = \code{'darkorchid'})
#' color for the axes.
#' @param alpha.axes
#' (Default = .2) transparency factor for the
#' color of the axes.
#' @param width.axes (Default = 1.1) the width of the axes
#' @param col.background
#' [Default = \code{adjustcolor('lavender', alpha.f = .2)}],
#' The color of the background.
#' @param ... eveythings else for the functions.
#' @return a list with
#' \code{baseMap_S:} The Background (Symmetric)
#' \code{I_labels_S} The labels I-set (Symmetric).
#' \code{I_points_S} The dots I-set (Symmetric).
#' \code{J_labels_S} The labels J-set (Symmetric).
#' \code{J_points_S} The dots J-set(Symmetric).
#' \code{baseMap_A} The Background (Asymmetric)
#' \code{I_labels_A} The labels I-set (Asymmetric).
#'\code{I_points_A} The dots I-set (Asymmetric).
#' \code{J_labels_A} The labels J-set (Asymmetric).
#' \code{J_points_A} The dots J-set (Asymmetric).
#' \code{baseMap_B} The Background (Barycentric).
#' \code{I_labels_B} The labels I-set (Barycentric).
#' \code{I_points_B} The dots I-set (Barycentric).
#' \code{J_labels_B} The labels J-set (Barycentric).
#' \code{J_points_B} The dots J-set (Barycentric).
#; NB class = 'createAllMaps4CA'
#' @details The final maps are built
#' by combining the elementary maps.
#' For example, a map with the \eqn{J}-set being asymmetric
#' and the \eqn{I}-set being Symmetric would be made
#' by creating the \code{Ja_Is} map as
#' \code{Ja_Is <- baseMap_A + J_labels_A + I_labels_S}.
#'
#' Note than, in general, the \code{Asymmetric} is larger than the
#' \code{Symmetric} map which is in turn larger than the
#' \code{Barycentric} map.
#' @section Important_Note:
#' When creating multiple layers graphs,
#' because of the way \code{ggplot2} create graphs,
#' all
#' the matrices/dataframe should all the have
#' the same column names
#' [e.g., \code{colnames()}
#' 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").
#' @export
# @examples \dontrun{}
#' @author Hervé Abdi
#' @seealso createFactorMaps createbaseMap
createAllMaps4CA <- function(allNormedFactors,
# A list with all the
# factor scores normed
# typically from createAllNormedFactors
axis1 = 1, axis2 = 2,
# defaultnames for the graphs
# constraints = NULL,
# list with minx miny maxx maxy
# as obtained, e.g.,
# from minmacHelper from prettyGraphs
title = NULL,
# The I-set
col.points.i = 'blueviolet',
#display.points.i = TRUE,
alpha.points.i = .5,
pch.i = 19, # Character for the dots
# 19 is circle
cex.i = 2.5, # size of the dots
segment.size.i = 0, # size of segment
#display.labels.i = TRUE,
col.labels.i = 'darkorchid4',
alpha.labels.i = 1, # alapha for text
text.cex.i = 4, # font size for labels
font.face.i = 'bold', # font for labels
font.family.i = 'sans' ,
force.i = 1 , # force repel factor for ggrepel
# The J-set
col.points.j = 'darkolivegreen4',
alpha.points.j = .5,
#display.points.j = TRUE,
pch.j = 18, # Character for the dots
# 18 is diamond
cex.j = 2.5, # size of the dots
segment.size.j = 0, # size of segment
#display.labels.j = TRUE,
col.labels.j = 'darkolivegreen',
alpha.labels.j = 1,
text.cex.j = 4, # font size for labels
font.face.j = 'bold', # font for labels
font.family.j = 'sans' ,
# font family for labels
force.j = 1 , # force repel factor for ggrepel
col.axes = 'darkorchid',
# color for the axes
alpha.axes = .2,
# tranparency for the axes
width.axes = 1.1,
# width of the axes
col.background =
adjustcolor('lavender',
alpha.f = .2),
# background color
... # more stuff
){
# Start with symmetric
#
Fi_S <- allNormedFactors$Fi[,c(axis1,axis2)]
Fj_S <- allNormedFactors$Fj[,c(axis1,axis2)]
# constraints_S <- minmaxHelper(Fi_S, Fj_S)
Maps_S <-
createFactorMapIJ(Fi_S,Fj_S,
axis1 = axis1, axis2 = axis2,
constraints = NULL,
# list with minx miny maxx maxy
# as obtained, e.g.,
# from minmacHelper from prettyGraphs
title = title,
# The I-set
col.points.i = col.points.i,
alpha.points.i = alpha.points.i,
#display.points.i = TRUE,
pch.i = pch.i, # Character for the dots
cex.i = cex.i, # size of the dots
#display.labels.i = TRUE,
col.labels.i = col.labels.i,
alpha.labels.i = alpha.labels.i,
text.cex.i = text.cex.i, # font size for labels
font.face.i = font.face.i , # font for labels
font.family.i = font.family.i,
# The J-set
col.points.j = col.points.j,
alpha.points.j = alpha.points.j,
#display.points.j = TRUE,
pch.j = pch.j, # Character for the dots
cex.j = cex.j, # size of the dots
#display.labels.j = TRUE,
col.labels.j = col.labels.j,
alpha.labels.j = alpha.labels.j,
text.cex.j = text.cex.j, # font size for labels
font.face.j = font.face.j, # font for labels
font.family.j = font.family.j ,
# font family for labels
col.axes = col.axes,
# color for the axes
alpha.axes = alpha.axes,
# tranparency for the axes
width.axes = width.axes,
# width of the axes
col.background = col.background ,
# background color
... # more stuff
)
# Asymetric Maps
#
Fi_A <- allNormedFactors$Fi_A[,c(axis1,axis2)]
Fj_A <- allNormedFactors$Fj_A[,c(axis1,axis2)]
# constraints_S <- minmaxHelper(Fi_S, Fj_S)
Maps_A <-
createFactorMapIJ(Fi_A,Fj_A,
axis1 = axis1, axis2 = axis2,
constraints = NULL,
# list with minx miny maxx maxy
# as obtained, e.g.,
# from minmacHelper from prettyGraphs
title = title,
# The I-set
col.points.i = col.points.i,
alpha.points.i = alpha.points.i,
#display.points.i = TRUE,
pch.i = pch.i, # Character for the dots
cex.i = cex.i, # size of the dots
#display.labels.i = TRUE,
col.labels.i = col.labels.i,
alpha.labels.i = alpha.labels.i ,
text.cex.i = text.cex.i, # font size for labels
font.face.i = font.face.i , # font for labels
font.family.i = font.family.i,
# The J-set
col.points.j = col.points.j,
alpha.points.j = alpha.points.j,
#display.points.j = TRUE,
pch.j = pch.j, # Character for the dots
cex.j = cex.j, # size of the dots
#display.labels.j = TRUE,
col.labels.j = col.labels.j,
alpha.labels.j = alpha.labels.j,
text.cex.j = text.cex.j, # font size for labels
font.face.j = font.face.j, # font for labels
font.family.j = font.family.j ,
# font family for labels
col.axes = col.axes,
# color for the axes
alpha.axes = alpha.axes,
# tranparency for the axes
width.axes = width.axes,
# width of the axes
col.background = col.background ,
# background color
... # more stuff
)
# True Barycentric Maps
#
Fi_B <- allNormedFactors$Fi_B[,c(axis1,axis2)]
Fj_B <- allNormedFactors$Fj_B[,c(axis1,axis2)]
# constraints_S <- minmaxHelper(Fi_S, Fj_S)
Maps_B <-
createFactorMapIJ(Fi_B,Fj_B,
axis1 = axis1, axis2 = axis2,
constraints = NULL,
# list with minx miny maxx maxy
# as obtained, e.g.,
# from minmacHelper from prettyGraphs
title = title,
# The I-set
col.points.i = col.points.i,
alpha.points.i = alpha.points.i,
#display.points.i = TRUE,
pch.i = pch.i, # Character for the dots
cex.i = cex.i, # size of the dots
#display.labels.i = TRUE,
col.labels.i = col.labels.i,
alpha.labels.i = alpha.labels.i,
text.cex.i = text.cex.i, # font size for labels
font.face.i = font.face.i , # font for labels
font.family.i = font.family.i,
# The J-set
col.points.j = col.points.j,
alpha.points.j = alpha.points.j,
#display.points.j = TRUE,
pch.j = pch.j, # Character for the dots
cex.j = cex.j, # size of the dots
#display.labels.j = TRUE,
col.labels.j = col.labels.j,
alpha.labels.j = alpha.labels.j,
text.cex.j = text.cex.j, # font size for labels
font.face.j = font.face.j, # font for labels
font.family.j = font.family.j ,
# font family for labels
col.axes = col.axes,
# color for the axes
alpha.axes = alpha.axes,
# tranparency for the axes
width.axes = width.axes,
# width of the axes
col.background = col.background ,
# background color
... # more stuff
)
return.list = structure(list(baseMap_S = Maps_S$baseMap,
I_labels_S = Maps_S$I_labels,
I_points_S = Maps_S$I_points,
J_labels_S = Maps_S$J_labels,
J_points_S = Maps_S$J_points,
baseMap_A = Maps_A$baseMap,
I_labels_A = Maps_A$I_labels,
I_points_A = Maps_A$I_points,
J_labels_A = Maps_A$J_labels,
J_points_A = Maps_A$J_points,
baseMap_B = Maps_B$baseMap,
I_labels_B = Maps_B$I_labels,
I_points_B = Maps_B$I_points,
J_labels_B = Maps_B$J_labels,
J_points_B = Maps_B$J_points
),
class = 'createAllMaps4CA')
return(return.list)
}
#_____________________________________________________________________
# Change the print function for
# the createAllMaps4CA environment
#
#' Change the print function for createAllMaps4CA
#'
#' Change the print function for createAllMaps4CA
#'
#' @param x a list: output of createAllMaps4CA
#' @param ... everything else for the functions
#' @author Herve Abdi
#' @export
print.createAllMaps4CA <- function (x, ...) {
ndash = 78 # How many dashes for separation lines
cat(rep("-", ndash), sep = "")
cat("\nBasemaps and Point and Labels maps for Correspondence Analysis ")
cat("\nThree Normalizations: Symmetric, Asymmetric, and True Barycentric ")
cat("\nOne Mais is Basemap + dots and / or Labels \n ")
# cat("\n List name: ",deparse(eval(substitute(substitute(x)))),"\n")
cat(rep("-", ndash), sep = "")
cat("\n Symmetric Maps (Inertia = Lambda) \n")
cat(rep("-", ndash), sep = "")
cat("\n$baseMap_S ", "The Base Map to which the subMaps are added")
cat("\n$I_labels_S ", "I-Set (row) Labels")
cat("\n$I_points_S ", "I-Set (row) Points")
cat("\n$J_labels_S ", "J-Set (col) Labels")
cat("\n$J_points_S ", "J-Set (col) Points")
cat("\n",rep("-", ndash), sep = "")
cat("\n Asymmetric Maps (Inertia = Unity) \n")
cat(rep("-", ndash), sep = "")
cat("\n$baseMap_A ", "The Base Map to which the subMaps are added")
cat("\n$I_labels_A ", "I-Set (row) Labels")
cat("\n$I_points_A ", "I-Set (row) Points")
cat("\n$J_labels_A ", "J-Set (col) Labels")
cat("\n$J_points_A ", "J-Set (col) Points")
cat("\n",rep("-", ndash), sep = "")
cat("\n True Barycentric Maps (Inertia = Lambda^2) \n")
cat(rep("-", ndash), sep = "")
cat("\n$baseMap_B ", "The Base Map to which the subMaps are added")
cat("\n$I_labels_B ", "I-Set (row) Labels")
cat("\n$I_points_B ", "I-Set (row) Points")
cat("\n$J_labels_B ", "J-Set (col) Labels")
cat("\n$J_points_B ", "J-Set (col) Points")
cat("\n",rep("-", ndash), sep = "")
cat("\n",rep("-", ndash), sep = "")
cat("\n")
invisible(x)
} # end of function print.createAllMaps4CA
#_____________________________________________________________________
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.