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
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),
.tiff file is created.
For 'publication' plots, if neither
are provided, the plot is displayed to the default graphics
device (usually a new window). If both
ext are provided, a file of type
ext is created
If only one of
ext is given, an error is
In either case, the file extension will automatically be
appended to the end of
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
file = ~/my/path, the file will be called
Furthermore, some of the 'publication' quality plots allow for
ggplot2 argument. If
then the plot will be produced using the
ggplot object will be returned. This allows for
additional, personal customization of the plot for those who
have used the package before. If
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
file is given without a directrory
file = my_fancy_file), then that file will be
created in the current working directory (see
?setwd for more information).
The current default resolution is 1000 dpi for all plots.
Wen Chen and Joshua Simpson.
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