plot.TRAMPknowns {TRAMPR}

Summary Plot of Knowns Data

Description

Creates a plot showing the clustering and profiles of a TRAMPknowns object (a “knowns database”). The plot has three vertical panels;

• The leftmost contains a dendrogram, showing how similar the profiles of knowns are (see group.knowns for details).

• The rightmost displays the TRFLP profile for each individual (with a different colour symbol for each different enzyme/primer combination).

• The middle panel displays information on the species names and groups of the knowns.

Usage

## S3 method for class 'TRAMPknowns'
plot(x, cex=1, name="species", pch=1, peaks.col, p=.02,
     group.clusters=TRUE, groups.col=1:4, grid.by=5, grid.col="gray",
     widths=c(1, 2, 1), ...)

Arguments

x

A TRAMPknowns object.

cex

Character size for the plot. Because knowns databases can be large, this should be small and may need to be adjusted. Most aspects of the plot will scale with this.

name

Column name to use when generating species names; must be one of species or group.name.

pch

Plotting symbol to use for peaks in the peak profiles.

peaks.col

Vector of colours to plot the different enzymes in the peak profiles. These will be used in the order of the columns of summary(x).

p

Scaling factor for the middle plot; this specifies the proportion of the width that elements are spaced horizontally from one another. Columns of text are p apart, brackets grouping knowns are p/2 apart, and cluster groups (if present) are p*2/3 apart.

group.clusters

Logical: Should groups of clusters (determined by group.strict - see group.knowns) be joined together?

groups.col

Vector of colours to plot different group clusters in. This will be recycled as neccessary.

grid.by

Interval between horizontal grid lines. Grid lines start at ceiling(grid.by/2) from the bottom of the plot. A value of NA suppresses grid lines.

grid.col

Colour of the horizontal grid lines.

widths

Relative widths of the three panels of the plot (see layout). widths must be a vector of 3 elements, corresponding to the three panels from left to right.

...

Additional arguments (ignored).

Note

In general, there will probably be too many knowns to make a legible plot when displayed on the screen. We recommend creating a PDF of the plot and viewing that instead (see Example).

When plotted on the interactive plotting device, if the plot is resized, the plot is likely to look strange.

See Also

group.knowns, which controls the grouping of knowns, and TRAMPknowns, which constructs TRAMPknowns objects.

Examples

data(demo.knowns)
plot(demo.knowns)

## Not run: 
pdf("knowns_summary.pdf", paper="default", width=8, height=11)
plot(demo.knowns)
plot(demo.knowns, group.clusters=FALSE)
dev.off()

## End(Not run)