Description Overview ggplot2 File Types Note See Also Author(s)
This help page details the standards for RAM plotting functions.
The RAM package contains many functions to produce plots and
visualizations for metagenomic data. Currently, the plotting
functions are grouped into 'casual' and 'publication' categories.
The 'casual' plotting functions only accept a file
argument and produce a .tiff
file automatically. They
are meant to quickly highlight certain aspects of the data, but
are not meant to be published. The 'publication' quality plots
accept many more graphing parameters, and should be of suitable
quality for future publication. All 'publication' plots should
accept the following parameters, in addition to those required
to produce the plot:
"file"
the file name for the plot.
"ext"
the file type for the plot (see below).
"height"
the height of the plot, in inches.
"width"
the width of the plot, in inches.
Additionally, the following parameters are accepted by some functions:
"bw"
should the plot be in black and white?
For 'casual' plots, if file
is not provided, the plot is
displayed to the default graphics device (usually a new window),
otherwise a .tiff
file is created.
For 'publication' plots, if neither file
nor ext
are provided, the plot is displayed to the default graphics
device (usually a new window). If both file
and
ext
are provided, a file of type ext
is created
at file
.
If only one of file
or ext
is given, an error is
raised.
In either case, the file extension will automatically be
appended to the end of file
, if file
does not
already end in the appropriate extension.
For example, if file = ~/my/path.tiff
and
ext = png
, the file will be called
~/my/path.tiff.png
; but if file = ~/my/path.png
,
the file will just be called ~/my/path.png
.
Finally, if file = ~/my/path
, the file will be called
~/my/path.png
.
Furthermore, some of the 'publication' quality plots allow for
a ggplot2
argument. If ggplot2
is TRUE
,
then the plot will be produced using the ggplot2
package,
and a ggplot
object will be returned. This allows for
additional, personal customization of the plot for those who
have used the package before. If ggplot2
is FALSE
,
then the plot will be created using the base plotting functions.
For 'publication' quality plots, the following file types are
supported (use any of the following values for the ext
argument): "pdf"
, "png"
, "tiff"
,
"svg"
, "bmp"
, "jpeg"
.
If file
is given without a directrory
(e.g. file
= my_fancy_file), then that file will be
created in the current working directory (see ?getwd
and
?setwd
for more information).
The current default resolution is 1000 dpi for all plots.
Wen Chen and Joshua Simpson.
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