Skip to contents

Create Colourkey

create.colourkey.Rd

A function for generating and placing a colour key. Good for use in multiplots when a smaller colour key is desired.

Usage

create.colourkey(
  x,
  scale.data = FALSE,
  colour.scheme = c(),
  total.colours = 99,
  colour.centering.value = 0,
  colour.alpha = 1,
  fill.colour = 'darkgray',
  at = NULL,
  colourkey.labels.at = NULL,
  colourkey.labels = colourkey.labels.at,
  colourkey.labels.cex = 1,
  placement = NULL
  );

Arguments

x

Either a data-frame or a matrix from which the heatmap was created

scale.data

Was the data for the heatmap scaled? Defaults to FALSE.

colour.scheme

Heatmap colouring. Accepts old-style themes, or a vector of either two or three colours that are gradiated to create the final palette.

total.colours

Total number of colours to plot.

colour.centering.value

The center of the colour-map.

colour.alpha

Bias to be added to colour selection (uses x^colour.alpha in mapping).

fill.colour

The background fill (only exposed where missing values are present.

at

A vector specifying the breakpoints along the range of x.

colourkey.labels.at

A vector specifying the tick-positions on the colourkey.

colourkey.labels

A vector specifying tick-labels of the colourkey

colourkey.labels.cex

Size of colourkey labels. Defaults to 1

placement

Location and size of the colourkey.

Value

Returns a key in the format specified in the xyplot documentation.

Author

Stephenie Prokopec

See also

xyplot, plotmath

Examples

set.seed(1234567890);
x <- outer(-5:5, -5:5, '*') + matrix(nrow = 11, ncol = 11, data = runif(11 * 11));
colnames(x) <- paste('col', 1:11, sep = '-');
rownames(x) <- paste('row', 1:11, sep = '-');

y <- as.data.frame(x);
y$mean <- apply(x,1,mean);

# example of a simple multiplot with colourkey
heatmap1 <- create.heatmap(
    x = t(x),
    filename = NULL,
    clustering.method = 'none',
    scale.data = FALSE,
    yaxis.lab = NA,
    print.colour.key = FALSE,
    colour.scheme = c('chartreuse3', 'white', 'blue'),
    at = seq(-25, 25, 0.01)
    );
#> Warning: max(x) = 25.9832547025289 is greater than max(at) =  25 Clipped data will be plotted

barplot1 <- create.barplot(
    1:nrow(y) ~ mean,
    y,
    plot.horizontal = TRUE
    );

create.multiplot(
    plot.objects = list(heatmap1, barplot1),
    # filename = tempfile(pattern = 'multiplot_with_colourkey', fileext = '.tiff'),
    plot.layout = c(2,1),
    panel.widths = c(2,1),
    yat = list(1:nrow(y), NULL),
    yaxis.labels = rownames(y),
    xlimits = list(NULL, c(0,1)),
    xat = list(NULL, seq(0,1,0.5)),
    xaxis.labels = list(NULL, seq(0,1,0.5)),
    x.spacing = 0,
    print.new.legend = TRUE,
    legend = list(
        inside = list(
            fun = BoutrosLab.plotting.general::create.colourkey(
                x = x,
                colour.scheme = c('chartreuse3', 'white', 'blue'),
                at = seq(-25, 25, 0.01),
                colourkey.labels.at = c(-25, 0, 25),
                placement = viewport(just = 'left', x = 0.55, y = -0.55, width = 0.5)
                )
            )
        ),
    bottom.padding = 4,
    width = 10,
    height = 8,
    resolution = 500
    );
#> Warning: max(x) = 25.9832547025289 is greater than max(at) =  25 Clipped data will be plotted

#> Warning: number of items to replace is not a multiple of replacement length
#> Warning: number of items to replace is not a multiple of replacement length