Description Usage Arguments Note See Also Examples
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.
1 2 3 4 |
x |
A |
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 |
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 |
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 |
group.clusters |
Logical: Should groups of clusters (determined
by |
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 |
grid.col |
Colour of the horizontal grid lines. |
widths |
Relative widths of the three panels of the plot (see
|
... |
Additional arguments (ignored). |
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.
group.knowns
, which controls the grouping of
knowns, and TRAMPknowns
, which constructs
TRAMPknowns
objects.
1 2 3 4 5 6 7 8 9 10 | 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)
|
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