cyt_bp

This function creates a PDF file containing box plots for the continuous
variables in the provided data. If the number of columns in <code>data</code> exceeds
<code>bin.size</code>, the function splits the plots across multiple pages.

Provides comprehensive cytokine profiling analysis through quality control using biologically meaningful cutoffs on raw cytokine measurements and by testing for distributional symmetry to recommend appropriate transformations. Offers exploratory data analysis with summary statistics, enhanced boxplots, and barplots, along with univariate and multivariate analytical capabilities for in-depth cytokine profiling such as Principal Component Analysis based on Andrzej Maćkiewicz and Waldemar Ratajczak (1993) <doi:10.1016/0098-3004(93)90090-R>, Sparse Partial Least Squares Discriminant Analysis based on Lê Cao K-A, Boitard S, and Besse P (2011) <doi:10.1186/1471-2105-12-253>, Random Forest based on Breiman, L. (2001) <doi:10.1023/A:1010933404324>, and Extreme Gradient Boosting based on Tianqi Chen and Carlos Guestrin (2016) <doi:10.1145/2939672.2939785>.

Shubh Saraswat

CytoProfile

Cytokine Profiling Analysis Tool

Xiaohua Douglas Zhang

cyt_bp function

<dl><dt>data</dt>
<dd>A matrix or data frame containing the raw data to be plotted.</dd>
<dt>pdf_title</dt>
<dd>A string representing the name of the PDF file to
be created. If set to <code>NULL</code>, the box plots are displayed on the current
graphics device. Default is <code>NULL</code>.</dd>
<dt>bin_size</dt>
<dd>An integer specifying the maximum number of box plots to
display on a single page.</dd>
<dt>y_lim</dt>
<dd>An optional numeric vector defining the y-axis limits
for the plots.</dd>
<dt>scale</dt>
<dd>An optional character string. If set to "log2",
numeric columns are log2-transformed.</dd></dl>

Arguments

Author

Boxplots for Overall Comparisons by Continuous Variables. — cyt_bp

<dl>

<dt>data</dt>
<dd>A matrix or data frame containing the raw data to be plotted.</dd>


<dt>pdf_title</dt>
<dd>A string representing the name of the PDF file to
be created. If set to <code>NULL</code>, the box plots are displayed on the current
graphics device. Default is <code>NULL</code>.</dd>


<dt>bin_size</dt>
<dd>An integer specifying the maximum number of box plots to
display on a single page.</dd>


<dt>y_lim</dt>
<dd>An optional numeric vector defining the y-axis limits
for the plots.</dd>


<dt>scale</dt>
<dd>An optional character string. If set to "log2",
numeric columns are log2-transformed.</dd>

</dl>

cyt_bp: Boxplots for Overall Comparisons by Continuous Variables.

Description

Usage

Value

Arguments

Author

Examples