contrasting_color

Function picks colors to contrast with the colors given as the <code>'col'</code> argument.

Create networks of gene sets, infer clusters of functionally-related gene sets based
on similarity statistics, and visualize the results. This package simplifies and accelerates
interpretation of pathways analysis data sets. It is designed to work in tandem with standard
pathways analysis methods, such as the 'GSEA' program (Gene Set Enrichment Analysis), CERNO
(Coincident Extreme Ranks in Numerical Observations, implemented in the 'tmod' package) and others.
Inputs to 'GSNA' are the outputs of pathways analysis methods: a list of gene sets (or "modules"),
pathways or GO-terms with associated p-values. Since pathways analysis methods may be used to
analyze many different types of data including transcriptomic, epigenetic, and high-throughput
screen data sets, the 'GSNA' pipeline is applicable to these data as well. The use of 'GSNA' has
been described in the following papers:
Collins DR, Urbach JM, Racenet ZJ, Arshad U, Power KA, Newman RM, et al. (2021) <doi:10.1016/j.immuni.2021.08.007>,
Collins DR, Hitschfel J, Urbach JM, Mylvaganam GH, Ly NL, Arshad U, et al. (2023) <doi:10.1126/sciimmunol.ade5872>.

Jonathan M Urbach

GSNA

Gene Set Networking Analysis Package

contrasting_color function

<dl><dt>col</dt>
<dd>A character vector of colors.</dd>
<dt>type</dt>
<dd>(optional) Type of contrasting color, i.e. the method of generating the contrasting color.
Valid values are <code>'complement'</code>, <code>'rotate'</code>, <code>'yellow'</code>, <code>'gray'</code>, <code>'binary'</code>
and <code>'blackyellow'</code>.</dd>
<dt>threshold</dt>
<dd>(optional, used only for <code>type='binary'</code>) The "binary" method works by assessing
the mean value of the RGB channels. If the value is above a threshold, the low color is returned, if it
is below the threshold, the high color is returned.</dd>
<dt>low</dt>
<dd>(optional, used only for <code>type='binary'</code>) Low color (see <code>threshold</code> argument).</dd>
<dt>high</dt>
<dd>(optional, used only for <code>type='binary'</code>) High color (see <code>threshold</code> argument).</dd></dl>

Arguments

contrasting_color — contrasting_color

<dl>

<dt>col</dt>
<dd>A character vector of colors.</dd>


<dt>type</dt>
<dd>(optional) Type of contrasting color, i.e. the method of generating the contrasting color.
Valid values are <code>'complement'</code>, <code>'rotate'</code>, <code>'yellow'</code>, <code>'gray'</code>, <code>'binary'</code>
and <code>'blackyellow'</code>.</dd>


<dt>threshold</dt>
<dd>(optional, used only for <code>type='binary'</code>) The "binary" method works by assessing
the mean value of the RGB channels. If the value is above a threshold, the low color is returned, if it
is below the threshold, the high color is returned.</dd>


<dt>low</dt>
<dd>(optional, used only for <code>type='binary'</code>) Low color (see <code>threshold</code> argument).</dd>


<dt>high</dt>
<dd>(optional, used only for <code>type='binary'</code>) High color (see <code>threshold</code> argument).</dd>

</dl>

contrasting_color: contrasting_color

Description

Usage

Value

Arguments