statres_histogram

Plots a histogram indicating the number of significant
biomolecules, grouped by test type and fold change direction.

internal

Provides functionality for quality control processing and statistical analysis of mass spectrometry (MS) omics data, in particular proteomic (either at the peptide or the protein level), lipidomic, and metabolomic data, as well as RNA-seq based count data and nuclear magnetic resonance (NMR) data. This includes data transformation, specification of groups that are to be compared against each other, filtering of features and/or samples, data normalization, data summarization (correlation, PCA), and statistical comparisons between defined groups. Implements methods described in: Webb-Robertson et al. (2014) <doi:10.1074/mcp.M113.030932>. Webb-Robertson et al. (2011) <doi:10.1002/pmic.201100078>. Matzke et al. (2011) <doi:10.1093/bioinformatics/btr479>. Matzke et al. (2013) <doi:10.1002/pmic.201200269>. Polpitiya et al. (2008) <doi:10.1093/bioinformatics/btn217>. Webb-Robertson et al. (2010) <doi:10.1021/pr1005247>.

Lisa Bramer

pmartR

Panomics Marketplace - Quality Control and Statistical Analysis
for Panomics Data

Kelly Stratton

Daniel Claborne

Evan Glasscock

Rachel Richardson

David Degnan

Evan Martin

statres_histogram function

<dl><dt>x, fc_colors</dt>
<dd>passed from
<code>pmartR::plot.statRes()</code></dd>
<dt>text_size</dt>
<dd>An integer specifying the size of the text (number of
non-missing values) within the plot. The default is 3.
be displayed on the bar plot. The default is TRUE.</dd>
<dt>x_lab</dt>
<dd>character string specifying the x-axis label.</dd>
<dt>y_lab</dt>
<dd>character string specifying the y-axis label.</dd>
<dt>title_lab</dt>
<dd>character string specifying the plot title.</dd>
<dt>legend_lab</dt>
<dd>character string specifying the legend title.</dd>
<dt>free_y_axis</dt>
<dd>logical specifying whether to use <code>scales = 'free'</code> in <code><a href="https://ggplot2.tidyverse.org/reference/facet_wrap.html">ggplot2::facet_wrap</a></code></dd>
<dt>show_sig</dt>
<dd>logical specifying whether only significant fold changes
are included in the histogram or all fold changes</dd></dl>

Arguments

Fold change histogram for statres objects — statres_histogram

<dl>

<dt>x, fc_colors</dt>
<dd>passed from
<code>pmartR::plot.statRes()</code></dd>


<dt>text_size</dt>
<dd>An integer specifying the size of the text (number of
non-missing values) within the plot. The default is 3.
be displayed on the bar plot. The default is TRUE.</dd>


<dt>x_lab</dt>
<dd>character string specifying the x-axis label.</dd>


<dt>y_lab</dt>
<dd>character string specifying the y-axis label.</dd>


<dt>title_lab</dt>
<dd>character string specifying the plot title.</dd>


<dt>legend_lab</dt>
<dd>character string specifying the legend title.</dd>


<dt>free_y_axis</dt>
<dd>logical specifying whether to use <code>scales = 'free'</code> in <code><a href='https://ggplot2.tidyverse.org/reference/facet_wrap.html'>ggplot2::facet_wrap</a></code></dd>


<dt>show_sig</dt>
<dd>logical specifying whether only significant fold changes
are included in the histogram or all fold changes</dd>

</dl>

statres_histogram: Fold change histogram for statres objects

Description

Usage

Value

Arguments