make_barplot_on_synergy_subset_stats

integer vector with values the amount of models
that predicted each synergy subset, defined as a comma-separated string of
drug combinations in the names attribute of the vector

synergy.subset.stats

integer. Use it to discard elements of
the <code>synergy.subset.stats</code> vector that are strictly less than the
specified threshold

threshold.for.subset.removal

integer used to vertically fit in the names of the drug
combinations in the x-axis (specified in inches). The best <code>bottom.margin</code>
value depends on the maximum size of a synergy subset as defined in the
<code>names</code> attribute of the <code>synergy.subset.stats</code>.
Some rules of thumb are:
size = 1 =&gt; bottom.margin = 4,
size = 2 =&gt; bottom.margin = 6,
size = 3 =&gt; bottom.margin = 9,
size = 4 =&gt; bottom.margin = 12, etc.

bottom.margin

string. The name of the cell line to be used in the title
of the produced plot. Default value: NULL (the cell line name will not be
added to the title).

cell.line

Use this function to easily make a barplot that shows the amount of models
that predicted each synergy subset out of the set of all observed synergies.

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.

make_barplot_on_synergy_subset_stats: Bar plot of observed synergy subsets

Description

Usage

Arguments