Display 2D tour projections displayed separately by groups

This function is designed to allow comparisons across multiple groups, especially for examining things like two (or more) different models on the same data. The primary display is a scatterplot, with lines or contours overlaid.

Usage

display_groupxy(
  centr = TRUE,
  axes = "center",
  half_range = NULL,
  col = "black",
  pch = 20,
  cex = 1,
  edges = NULL,
  edges.col = "black",
  edges.width = 1,
  group_by = NULL,
  plot_xgp = TRUE,
  palette = "Zissou 1",
  shapeset = c(15:17, 23:25),
  axislablong = FALSE,
  ...
)

animate_groupxy(data, tour_path = grand_tour(), ...)

Arguments

centr

if TRUE, centers projected data to (0,0). This pins the center of data cloud and make it easier to focus on the changing shape rather than position.

axes

position of the axes: center, bottomleft or off

half_range

half range to use when calculating limits of projected. If not set, defaults to maximum distance from origin to each row of data.

col

color to use for points, can be a vector or hexcolors or a factor. Defaults to "black".

pch

shape of the point to be plotted. Defaults to 20.

cex

size of the point to be plotted. Defaults to 1.

edges

A two column integer matrix giving indices of ends of lines.

edges.col

colour of edges to be plotted, Defaults to "black"

edges.width

line width for edges, default 1

group_by

variable to group by. Must have less than 25 unique values.

plot_xgp

if TRUE, plots points from other groups in light grey

palette

name of color palette for point colour, used by hcl.colors, default "Zissou 1"

shapeset

numbers corresponding to shapes in base R points, to use for mapping categorical variable to shapes, default=c(15:17, 23:25)

axislablong

text labels only for the long axes in a projection, default FALSE

...

other arguments passed on to animate and display_groupxy

data

matrix, or data frame containing numeric columns

tour_path

tour path generator, defaults to 2d grand tour

Examples

animate_groupxy(flea[, 1:6], col = flea$species,
  pch = flea$species, group_by = flea$species)
#> Converting input data to the required matrix format.
#> Using half_range 4.4
#> Warning: "shapes" is not a graphical parameter
#> Warning: "shapes" is not a graphical parameter
#> Warning: "shapes" is not a graphical parameter

#> Warning: "shapes" is not a graphical parameter
#> Warning: "shapes" is not a graphical parameter
#> Warning: "shapes" is not a graphical parameter

animate_groupxy(flea[, 1:6], col = flea$species,
  pch = flea$species, group_by = flea$species,
  plot_xgp = FALSE)
#> Converting input data to the required matrix format.
#> Using half_range 4.4


# Edges example
x <- data.frame(x1=runif(10, -1, 1), x2=runif(10, -1, 1), x3=runif(10, -1, 1))
x$cl <- factor(c(rep("A", 3), rep("B", 3), rep("C", 4)))
x.edges <- cbind(from=c(1,2, 4,5, 7,8,9), to=c(2,3, 5,6, 8,9,10))
x.edges.col <- factor(c(rep("A", 2), rep("B", 2), rep("C", 3)))
animate_groupxy(x[,1:3], col=x$cl, group_by=x$cl, edges=x.edges, edges.col=x.edges.col)
#> Converting input data to the required matrix format.
#> Using half_range 1.2
#> Warning: "shapes" is not a graphical parameter
#> Warning: "shapes" is not a graphical parameter
#> Warning: "shapes" is not a graphical parameter

#> Warning: "shapes" is not a graphical parameter
#> Warning: "shapes" is not a graphical parameter
#> Warning: "shapes" is not a graphical parameter