polar-class

An S4 class to define the polar coordinates and pvalues for polar
differential expression plots

Differential expression (DE) analysis can be used to discover quantitative changes in expression levels between experimental groups. Such results are typically visualised using volcano plots, however in cases where more than two experimental groups are involved, visualising results can become convoluted and it quickly becomes difficult to see the wood for the trees. This package provides easy-to-use functions to extract and visualise outputs from DE between three groups (primarily aimed at 'limma' and 'DESeq2' outputs). We present novel methods to map DE results into polar coordinates to enable users to combine and simultaneously view three sets of results. These graphics also possess optional 'plotly' outputs for interactive and three-dimensional functionality, as seen in Lewis et. al. (2019) <doi:10.1016/j.celrep.2019.07.091>.

Katriona Goldmann

volcano3D

Interactive Plotting of Three-Way Differential Expression
Analysis

Myles Lewis

polar-class function

<dl class="dl-horizontal">
<dt><code>sampledata</code></dt><dd>Sample data with ID and contrast column.</dd></dl><dt><code>contrast</code></dt><dd>The column name in `sampledata`` which contains the
three-group contrast factor used for comparisons.</dd><dt><code>pvalues</code></dt><dd>A data frame containing the p-values, and adjusted p-values,
for all three comparisons between groups in the 
contrast factor, as well as optional fold changes and multi-group tests.</dd><dt><code>multi_group_test</code></dt><dd>Column name prefix for statistical tests between
all three groups</dd><dt><code>expression</code></dt><dd>A data frame or matrix containing the expression data. This 
is used to calculate z-score and fold change, therefore it should be a 
normalised expression object such as log transformed or variance stabilised.</dd><dt><code>polar</code></dt><dd>A data frame containing:
<ul>
<li>The axis score or mean expression for each of the three groups 
 in comparison</li>
<li>The z-score polar coordinates: 'y_zscore', 'x_zscore' and 
 'r_zscore'</li>
<li>The fold-change polar coordinates: 'y_fc', 'x_fc' and 'r_fc'</li>
<li>'angle': The angle in radians for polar coordinates</li>
<li>'angle_degrees': The angle in degrees</li>
<li>'max_exp': The group with the highest expression</li>
<li>'sig': The significance category</li>
</ul></dd><dt><code>non_sig_name</code></dt><dd>The category name for variables which are not significant</dd>

polar-class: An S4 class to define the polar coordinates and pvalues for polar differential expression plots

Description

Arguments

Slots