plot_avg_state_diff_graph_vis

igraph graph object (to be translated to a visNetwork object)

numeric vector. Every value is in the [-1,1] interval and
represents the average activity difference of each node. The node names have
to be specified in the names attribute of the given vector. For example,
<code>diff</code> could be the result of using the function
<code><a rd-options="" href="/link/get_avg_activity_diff_based_on_specific_synergy_prediction?package=emba&version=0.1.1" data-mini-rdoc="emba::get_avg_activity_diff_based_on_specific_synergy_prediction">get_avg_activity_diff_based_on_specific_synergy_prediction</a></code>.

diff

a (nx2) numeric matrix of x-y coordinates (2 columns) for each
of the nodes (n) in the <code>net</code> igraph object

layout

string. The title of the visNetwork plot

title

This function uses the <code><a rd-options="visNetwork" href="/link/visNetwork?package=emba&version=0.1.1&to=visNetwork" data-mini-rdoc="visNetwork::visNetwork">visNetwork</a></code> package to plot a
network of nodes. The nodes are positioned according to the specified coordinates
given by the <code>layout</code> parameter and the colors are derived using the
<code>diff</code> values and the <code><a rd-options="" href="/link/get_node_colors?package=emba&version=0.1.1" data-mini-rdoc="emba::get_node_colors">get_node_colors</a></code> function. The color
of each node indicates how much more inhibited or active that node is, when
comparing the average model classified in the 'good' category vs the average
'bad' one.

Analysis and visualization of an ensemble of boolean models for
biomarker discovery in cancer cell networks. The package allows to easily
import the data results of a software pipeline that predicts synergistic drug
combinations in cancer cell lines, developed by the DrugLogics research group
in NTNU. It has generic functions that can be used to split a boolean model
dataset to model groups with regards to the models predictive performance (number of true
positive predictions or Matthews correlation coefficient score) or synergy prediction based on a given set
of observed synergies and find the average activity difference per network
node between all group pairs. Thus, given user-specific thresholds,
important nodes (biomarkers) can be accessed in the sense that they make the
models predict specific synergies (synergy biomarkers) or have better
performance in general (performance biomarkers). Lastly, if the
boolean models have a specific equation form and differ only in their link operator,
link operator biomarkers can also be assessed.

John Zobolas

emba

Ensemble Boolean Model Biomarker Analysis

plot_avg_state_diff_graph_vis function

numeric vector. Every value is in the [-1,1] interval and
represents the average activity difference of each node. The node names have
to be specified in the names attribute of the given vector. For example,
<code>diff</code> could be the result of using the function
<code><a rd-options='' href='get_avg_activity_diff_based_on_specific_synergy_prediction'>get_avg_activity_diff_based_on_specific_synergy_prediction</a></code>.

This function uses the <code><a rd-options='visNetwork' href='visNetwork'>visNetwork</a></code> package to plot a
network of nodes. The nodes are positioned according to the specified coordinates
given by the <code>layout</code> parameter and the colors are derived using the
<code>diff</code> values and the <code><a rd-options='' href='get_node_colors'>get_node_colors</a></code> function. The color
of each node indicates how much more inhibited or active that node is, when
comparing the average model classified in the 'good' category vs the average
'bad' one.

plot_avg_state_diff_graph_vis: Plot the graph of average state differences (visNetwork)

Description

Usage

Arguments

See Also