make_barplot_on_models_stats

table object, the result of using <a rd-options="base" href="/link/table?package=emba&version=0.1.1&to=base" data-mini-rdoc="base::table">table</a> on
a (numeric) vector. Usually it represents some models statistics summary -
counts for each TP prediction value for example.

models.stats

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

title

xlab

ylab

logical. If TRUE, the values of the x-axis will be trimmed
to 3 digits after the decimal point. Default value: FALSE.

cont.values

integer. Values from the <code>model.stats</code> that are less
or equal to the threshold will be pruned. Use it when there too many
categories and the graph appears too dense. Default value: 0

threshold

Use this function to produce a bar plot when the input is the result of using
the <a rd-options="base" href="/link/table?package=emba&version=0.1.1&to=base" data-mini-rdoc="base::table">table</a> function to a numeric vector

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

make_barplot_on_models_stats function

table object, the result of using <a rd-options='base' href='table'>table</a> on
a (numeric) vector. Usually it represents some models statistics summary -
counts for each TP prediction value for example.

Use this function to produce a bar plot when the input is the result of using
the <a rd-options='base' href='table'>table</a> function to a numeric vector

make_barplot_on_models_stats: Bar plot of model stats

Description

Usage

Arguments