Command-line usage
The wellmap
package comes with a command-line tool (also called
wellmap
) that displays a visual representation of the plate layout
described by a TOML file. This is meant to help catch mistakes, which can be
easy to make in complex layouts.
For more information on this command and its options, run:
$ wellmap -h
Visualize the plate layout described by a wellmap TOML file.
Usage:
wellmap <toml> [<param>...] [-o <path>] [-p] [-c <color>] [-s] [-f]
Arguments:
<toml>
TOML file describing the plate layout to display. For a complete
description of the file format, refer to:
https://wellmap.readthedocs.io/en/latest/file_format.html
<param>
The name(s) of one or more experimental parameters from the above TOML
file to project onto the plate. For example, if the TOML file contains
something equivalent to `well.A1.conc = 1`, then "conc" would be a
valid parameter name.
If no names are given, the default is to display any parameters that
have at least two different values. For complex layouts, this may
result in a figure too big to fit on the screen. The best solution for
this (at the moment) is just to specify some parameters to focus on.
Options:
-o --output PATH
Output an image of the layout to the given path. The file type is
inferred from the file extension. If the path contains a dollar sign
(e.g. '$.svg'), the dollar sign will be replaced with the base name of
the <toml> path.
-p --print
Print a paper copy of the layout, e.g. to reference when setting up an
experiment. The default printer for the system will be used. To see
the current default printer, run: `lpstat -d`. To change the default
printer, run: `lpoptions -d <printer name>`. When printing, the
default color scheme is changed to 'dimgray'. This can still be
overridden using the '--color' flag.
-c --color NAME
Use the given color scheme to illustrate which wells have which
properties. The given NAME must be one of the color scheme names
understood by either `matplotlib` or `colorcet`. See the links below
for the full list of supported colors, but some common choices are
given below. The default is 'rainbow':
rainbow: blue, green, yellow, orange, red
viridis: purple, green, yellow
plasma: purple, red, yellow
coolwarm: blue, red
tab10: blue, orange, green, red, purple, ...
dimgray: gray, black
Matplotlib colors:
https://matplotlib.org/examples/color/colormaps_reference.html
Colorcet colors:
http://colorcet.pyviz.org/
-s --superimpose
Superimpose the exact value for each well (i.e. as a word/number) above
the layout. Note that if the values are too big, they might overlap
neighboring wells, which could make things hard to read. If you want
more control over the exact formatting of these superimposed values,
use the python/R API.
-f --foreground
Don't attempt to return the terminal to the user while the GUI runs.
This is meant to be used on systems where the program crashes if run in
the background.