covariates.grob: Create one or more covariate bars

Description

Takes a list of covariate bar annotates and creates a grid graphical object for them

Usage

covariates.grob(
	covariates,
	ord,
	side = 'right',
	size = 1,
	grid.row = NULL,
	grid.col = NULL,
	grid.border = NULL,
	row.lines = NULL,
	col.lines = NULL,
	reorder.grid.index = FALSE,
        x = 0.5,
        y = 0.5
	);

Arguments

covariates

Any covariate annotate to add to the plot, as a fully formed list.

ord

A vector of integer indices indicating the order of the items in the covariate bars.

side

Intended position of the covariate bar when added as a legend. Allowed positions are “right” and “top”.

size

The size of each covariate bar in units of “lines”.

grid.row

A list of parameters to be passed to gpar specifying the behaviour of row lines in the covariate bars. See Notes for details.

grid.col

A list of parameters to be passed to gpar specifying the behaviour of column lines in the covariate bars.

grid.border

A list of parameters to be passed to gpar specifying the behaviour of the border around the covariate bars.

row.lines

Vector of row indices where grid lines should be drawn. If NULL (default), all row lines are drawn. Ignored if grid.row is not specified.

col.lines

Vector of column indices where grid lines should be drawn. If NULL (default), all column lines are drawn. Ignored if grid.col is not specified.

reorder.grid.index

Boolean specifying whether grid line indices should be re-ordered according to the ord argument. Defaults to FALSE.

x coordinate in npc coordinate system

y coordinate in npc coordinate system

Value

A grid graphical object (grob) representing the covariate bar(s)

Notes

This code is an adaptation of the dendrogramGrob function in the latticeExtra package. It uses functions of the grid package.

By default, the covariate bar grid is drawn via borders around individual rectangles using the parameters specified in the covariates argument (col, lwd, etc.). If grid.row, grid.col, or grid.border are specified by the user, additional grid lines are drawn over any existing ones using the parameters in these lists.

Examples

Run this code

# NOT RUN {
# }
# NOT RUN {
# create temp data
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 = '-');

# set covariates
covariate.colours1 <- x[,1]
covariate.colours1[covariate.colours1 >= 0] <- default.colours(3)[1];
covariate.colours1[covariate.colours1 != default.colours(3)[1]] <- default.colours(3)[2];

covariate.colours2 <- x[,1]
covariate.colours2[covariate.colours2 >= 0] <- default.colours(3)[2];
covariate.colours2[covariate.colours2 != default.colours(3)[2]] <- default.colours(3)[3];

# create an object to draw the covariates from
covariates1 <- list(
    rect = list(
        col = 'black',
        fill = covariate.colours1,
        lwd = 1.5
        ),
    rect = list(
        col = 'black',
        fill = covariate.colours2,
        lwd = 1.5
        )
    );

# create a covariates grob using a simple incremental ordering and default behaviour
covariates.grob1 <- covariates.grob(
    covariates = covariates1,
    ord = c(1:ncol(x)),
    side = 'right'
    );
tiff(
    file.path(tempdir(),'covariates_grob1.tiff'), 
    type = 'cairo', 
    width = 6, 
    height = 6, 
    units = 'in', 
    res = 1000, 
    compression = 'lzw'
    );
grid.draw(covariates.grob1);
dev.off();

# create a dendrogram for x
cov.dendrogram <- BoutrosLab.plotting.general::create.dendrogram(
    x = x,
    clustering.method = 'average'
    );

covariates2 <-list(
    rect = list(
        col = 'black',
        fill = covariate.colours2,
        lwd = 1.5
        )
    );

# create a covariates grob using the dendrogram ordering and double the default size
covariates.grob2 <- covariates.grob(
    covariates = covariates2,
    ord = order.dendrogram(cov.dendrogram),
    side = 'top',
    size = 2
    );
tiff(
    file.path(tempdir(),'covariates_grob2.tiff'), 
    type = 'cairo', 
    width = 6, 
    height = 6, 
    units = 'in', 
    res = 1000, 
    compression = 'lzw'
    );
grid.draw(covariates.grob2);
dev.off();

# add a border of a different colour
covariates.grob3 <- covariates.grob(
    covariates = covariates1,
    ord = c(1:ncol(x)),
    side = 'right',
    grid.border = list(col = 'red', lwd = 1.5)
    );
tiff(
    file.path(tempdir(),'covariates_grob3.tiff'), 
    type = 'cairo', 
    width = 6, 
    height = 6, 
    units = 'in', 
    res = 1000, 
    compression = 'lzw'
    );
grid.draw(covariates.grob3);
dev.off();

# create covariates with transparent rectangle borders
covariates3 <- list(
    rect = list(
        col = 'transparent',
        fill = covariate.colours1,
        lwd = 1.5
        ),
    rect = list(
        col = 'transparent',
        fill = covariate.colours2,
        lwd = 1.5
        )
    );

# add column grid lines and a border with default gpar settings
covariates.grob4 <- covariates.grob(
    covariates = covariates3,
    ord = c(1:nrow(x)),
    side = 'top',
    grid.col = list(col = 'black', lty = 3),
    grid.border = list()
    );
tiff(
    file.path(tempdir(),'covariates_grob4.tiff'), 
    type = 'cairo', 
    width = 6, 
    height = 6, 
    units = 'in', 
    res = 1000, 
    compression = 'lzw'
    );
grid.draw(covariates.grob4);
dev.off();

# draw a subset of row/column lines
covariates.grob5 <- covariates.grob(
    covariates = covariates3,
    ord = order.dendrogram(cov.dendrogram),
    side = 'right',
    grid.row = list(lineend = 'butt', lwd = 2),
    row.lines = 6,
    reorder.grid.index = FALSE, # note: this is already set by default
    grid.col = list(lty = 2),
    col.lines = c(0,1)
    );
tiff(
    file.path(tempdir(),'covariates_grob5.tiff'), 
    type = 'cairo', 
    width = 6, 
    height = 6, 
    units = 'in', 
    res = 1000, 
    compression = 'lzw'
    );
grid.draw(covariates.grob5);
dev.off();
# }