cyt_bp2

This function generates a PDF file containing boxplots for each combination
of numeric and factor variables in the provided data. It first converts
any character columns to factors and checks that the data contains at
least one numeric and one factor column. If the scale argument is set to
"log2", all numeric columns are log2-transformed. The function then
creates boxplots using ggplot2 for each numeric variable grouped by
each factor variable.

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_bp2 function

<dl><dt>data</dt>
<dd>A matrix or data frame of raw data.</dd>
<dt>pdf_title</dt>
<dd>A string representing the title
(and filename) of the PDF file. If <code>NULL</code>, the boxplots are displayed on the
current graphics device. Defaults to <code>NULL</code>.</dd>
<dt>scale</dt>
<dd>Transformation option for continuous variables.
Options are NULL (default) and "log2". When set to "log2",
numeric columns are transformed using the log2 function.</dd>
<dt>y_lim</dt>
<dd>An optional numeric vector defining the y-axis limits
for the plots.</dd></dl>

Arguments

Author

Boxplot Function Enhanced for Specific Group Comparisons. — cyt_bp2

<dl>

<dt>data</dt>
<dd>A matrix or data frame of raw data.</dd>


<dt>pdf_title</dt>
<dd>A string representing the title
(and filename) of the PDF file. If <code>NULL</code>, the boxplots are displayed on the
current graphics device. Defaults to <code>NULL</code>.</dd>


<dt>scale</dt>
<dd>Transformation option for continuous variables.
Options are NULL (default) and "log2". When set to "log2",
numeric columns are transformed using the log2 function.</dd>


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

</dl>

cyt_bp2: Boxplot Function Enhanced for Specific Group Comparisons.

Description

Usage

Value

Arguments

Author

Examples