plotby: Plot groups of genomes by release date

In cstubben/genomes2: Genome sequencing project metadata

Description

Plots the cumulative number of genomes by released date for different groups of genomes

Usage

plotby(x, groupby = "status", subset = NA, top = 5, 
labels = FALSE,  curdate=TRUE, abbrev = TRUE, flip = NA,
 legend = "topleft", lbty = "o", lcol = 1, ltitle = NULL, lcex = 1,
 lsort = TRUE, cex = 1, inset=0, ylim = NA, las = 1, lwd = 1, log = "", 
xlab = "Release Date", ylab = "Genomes", type='l',
col = c("blue", "red", "green3", "magenta", "yellow"), 
lty = 1:top, pch = c(15:18, 1:3), ...)

Arguments

x	a genomes data frame
groupby	a column name in the genomes table or a vector to group by
subset	logical vector indicating rows to keep
top	number of top groups to display
labels	plot a single line with labeled points using genome name column
curdate	include the current date on x-axis, if false, then default is range of release dates
abbrev	abbreviated genome names
flip	a number indicating where to flip labels from right to left, default is middle of plot
legend	a legend keyword or vector of x,y coordinates, defaults to top-left corner. Use NA for no legend
lbty	legend box type
lcol	number of columns in legend
ltitle	legend title
lcex	legend size expansion
inset	inset legend distances(s)
lsort	sort legend by decreasing order of genomes, default true
cex	label size expansion
ylim	y axis limits
las	rotate axis labels
lwd	line width
log	log scale
xlab	x axis label
ylab	y axis label
type	plot type
col	line or point colors
lty	line type
pch	point type
...	additional items passed to plot

Details

Two different plot types are available. The default is to plot multiple lines, one for each group (like matplot). If labels=TRUE, then a single line is drawn with different labeled points for each group.

Value

A plot of released dates by group

Author(s)

Chris Stubben

See Also

plot.genomes

Examples

data(proks)
# default group is status
plotby(proks, top=2)

## groupby can be a vector
plotby(proks, genus(proks$name), log='y', lcex=.7)

# OR plot labels
plotby(proks, subset=name %like% 'Haemophilus influenzae*', labels=TRUE, cex=.7, lbty='n')

cstubben/genomes2 documentation built on May 14, 2019, 12:25 p.m.