plotby: Plot groups of genomes by release date

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/plotby.R

Description

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

Usage

1
2
3
4
5
6
7
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

1
2
3
4
5
6
7
8
9
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 12, 2017, 1:19 p.m.