seriation (version 1.3.2)

pimage: Permutation Image Plot

Description

Provides methods for matrix shading, i.e., displaying a color image for matrix (including correlation matrices) and dist objects given an optional permutation. The plot arranges colored rectangles to represent the matrix value. Columns and rows appear in the order in the matrix. This visualization is also know asi a heatmap. Implementations based on the grid graphics engine and based n ggplot2 are provided.

Usage

# grid-based image plot
pimage(x, order = NULL, col = NULL, main ="", xlab = "", ylab = "",
  zlim = NULL, key = TRUE, keylab = "", symkey = TRUE,
  upper_tri = TRUE, lower_tri = TRUE, row_labels = NULL, col_labels = NULL,
  prop = TRUE, flip_axes = FALSE, reverse_columns = FALSE,
  ..., newpage = TRUE, pop = TRUE, gp = NULL)
# ggplot2-based image plot
ggpimage(x, order = NULL,
  upper_tri = TRUE, lower_tri = TRUE, row_labels = NULL, col_labels = NULL,
  prop = TRUE, flip_axes = FALSE, reverse_columns = FALSE)

Arguments

x

a matrix or an object of class dist.

order

an object of class ser_permutation. If NULL the order in x is plotted.

col

a list of colors used. If NULL, a gray scale is used (for matrix larger values are displayed darker and for dist smaller distances are darker). For matrices containing logical data, black and white is used. For matrices containing negative values a symmetric diverging color palette is used.

main

plot title.

xlab, ylab

labels for the x and y axes.

zlim

vector with two elements giving the range (min, max) for representing the values in the matrix.

key

logical; add a color key? No key is available for logical matrices.

keylab

string plotted next to the color key.

symkey

logical; if x contains negative values, should the color palate be symmetric (zero is in the middle)>

upper_tri, lower_tri

a logical indicating whether to show the upper or lower triangle of the distance matrix.

row_labels, col_labels

a logical indicating if row and column labels in x should be displayed. If NULL then labels are displayed if the x contains the appropriate dimname and the number of labels is 25 or less. A character vector of the appropriate length with labels can also be supplied.

prop

logical; change the aspect ratio so cells in the image have a equal width and height.

flip_axes

logical; exchange rows and columns for plotting.

reverse_columns

logical; revers the order of how the columns are displayed.

…

further arguments are ignored.

newpage, pop, gp

Start plot on a new page, pop the viewports after plotting, and use the supplied gpar object (see grid).

Details

Plots a matrix in its original row and column orientation. This means, in a plot the columns become the x-coordinates and the rows the y-coordinates (in reverse order).

If x is of class dist it is converted to full-storage representation before plotting.

Grid-based plot: The viewports used for plotting are called: "plot", "image" and "colorkey". Note: Since pimage uses grid, it should not be mixed with base R primitive plotting functions, but the appropriate functions in grid-package.

ggplot2-based plot: A ggplot2 object is returned. Colors, axis limits and other visual aspects can be added using standard ggplot2 functions (labs, scale_fill_continuous, labs, etc.).

See Also

grid-package, seriate, hmap, dissplot and image.

Examples

# NOT RUN {
x <- matrix(sample(c(FALSE, TRUE), 300, rep = TRUE), ncol = 10,
  dimnames = list(1:30, LETTERS[1:10]))

# Matrix for logical values. TRUE values are dark and no color key is shown. There are too many
# Row labels (>25) so they are suppressed.
pimage(x)

# Show all labels and flip axes or reverse columns
pimage(x, row_labels = TRUE, col_labels = TRUE, flip_axes = TRUE)
pimage(x, row_labels = TRUE, col_labels = TRUE, reverse_columns = TRUE)

# Reorder matrix, use custom colors, and add a title.
pimage(x, order = seriate(x), row_labels = TRUE, col_labels = TRUE,
  col = c("white", "red"), main = "Random Data (Reordered)")

# Show a reordered distance matrix (distances between rows).
# Dark means low distance. The aspect ratio is automatically fixed to 1:1.
# The upper triangle is suppressed triangle
d <- dist(x, method = "binary")
pimage(d,  order = seriate(d),
  main = "Random Data (Distances)")

# Show only distances that are smaller than .5 using limits on z.
pimage(d,  order = seriate(d),
  main = "Random Data (Distances + Theshold)", zlim = c(0, .5))

# Add to the plot using functions in package grid
library("grid")
pimage(x, pop = FALSE)           ### pop = FALSE allows us to manipulate viewports
downViewport(name = "image")

# Highlight cell column 7 (G) / row 5 (from top)/col with a red arrow starting at 5/2
# Note: columns are x and rows are y.
grid.lines(x = c(5, 7), y = c(2, 5), arrow = arrow(),
  default.units = "native", gp = gpar(col = "red", lwd = 3))

# add a red box around rows 15 and 16
grid.rect(x = 0.5, y = 15.5, width = ncol(x), height = 2,
  just = "left",
  default.units = "native", gp = gpar(col = "red", lwd = 3, fill = NA))

## remove the viewports
popViewport(0)

## put several pimages on a page (uses viewports and newpage = FALSE)
library(grid)
grid.newpage()
pushViewport(viewport(layout = grid.layout(nrow = 1, ncol = 2,
  widths = unit(c(.4, .6), unit = "npc"))))
pushViewport(viewport(layout.pos.row = 1, layout.pos.col = 1))

## seriate matrix
o <- seriate(x)
pimage(x, o, labCol = FALSE, main = "Random Data",
  newpage = FALSE)

upViewport(1)
pushViewport(viewport(layout.pos.row = 1, layout.pos.col = 2))

## add the reordered dissimilarity matrix for rows
d <- dist(x)
pimage(d, o[[1]], main = "Distances",
  newpage = FALSE)

upViewport(1)
popViewport(0)

## ggplot2 Examples
if (require("ggplot2")) {
  x <- matrix(sample(c(FALSE, TRUE), 300, rep = TRUE), ncol = 10,
    dimnames = list(1:30, LETTERS[1:10]))

  # Matrix for logical values. TRUE values are dark. There are too many
  # Row labels (>25) so they are suppressed.
  ggpimage(x)

  # Show all labels and flip axes or reverse columns
  ggpimage(x, flip_axes = TRUE, row_labels = TRUE, col_labels = TRUE)
  ggpimage(x, reverse_columns = TRUE, row_labels = TRUE, col_labels = TRUE)

  # Add lines
  ggpimage(x) +
    geom_hline(yintercept = seq(0, nrow(x)) + .5) +
    geom_vline(xintercept = seq(0, ncol(x)) + .5)

  # Reorder matrix, use custom colors, add a title,
  # and hide colorkey.
  ggpimage(x, order = seriate(x), row_labels = TRUE, col_labels = TRUE) +
    scale_fill_manual(values = c("grey90", "red")) +
    theme(legend.position = "none") +
    labs(title = "Random Data")


  # Show a reordered distance matrix (distances between rows).
  # Dark means low distance.
  d <- dist(x, method = "binary")
  ggpimage(d, order = seriate(d)) +
    labs(title = "Random Data", subtitle = "Distances")

  # Show also upper triangle
  ggpimage(d, order = seriate(d), upper_tri = TRUE) +
    labs(title = "Random Data", subtitle = "Distances")

  # Show only distances that are smaller than .5 using limits on fill.
  ggpimage(d,  order = seriate(d)) +
    labs(title = "Random Data (Distances + Theshold)") +
    scale_fill_gradient(low = "darkblue", high = "lightgray",
      limit = c(0, .5), na.value = "white")

  # Use ggplot2 themes with theme_set
  old_theme <- theme_set(theme_linedraw())
  ggpimage(d, order = seriate(d)) +
    labs(title = "Random Data (Distances)")
  theme_set(old_theme)

  # Use custom color palettes: Gray scale, Colorbrewer (provided in ggplot2) and colorspace
  ggpimage(d, order = seriate(d), upper_tri = FALSE) +
    scale_fill_gradient(low = "black", high = "white", na.value = "white")

  ggpimage(d, order = seriate(d), upper_tri = FALSE) +
    scale_fill_distiller(palette = "Spectral", direction = +1, na.value = "white")

  ggpimage(d, order = seriate(d), upper_tri = FALSE) +
    colorspace::scale_fill_continuous_sequential("Reds", rev = FALSE, na.value = "white")
}
# }