plot_mfi_for_analyte

Plot MFI value distribution for a given analyte

Speeds up the process of loading raw data from MBA (Multiplex Bead Assay) examinations, performs quality control checks, and automatically normalises the data, preparing it for more advanced, downstream tasks. The main objective of the package is to create a simple environment for a user, who does not necessarily have experience with R language. The package is developed within the project of the same name - 'PvSTATEM', which is an international project aiming for malaria elimination.

Tymoteusz Kwiecinski

PvSTATEM

Reading, Quality Control and Preprocessing of MBA (Multiplex
Bead Assay) Data

Jakub Grzywaczewski

Mateusz Nizwantowski

Przemyslaw Biecek

Nuno Sepulveda

plot_mfi_for_analyte function

<dl><dt>plate</dt>
<dd>A plate object</dd>
<dt>analyte_name</dt>
<dd>The analyte to plot</dd>
<dt>data_type</dt>
<dd>The type of data to plot. Default is "Median"</dd>
<dt>plot_type</dt>
<dd>The type of plot to generate. Default is "violin".
Available options are "boxplot" and "violin".</dd>
<dt>scale_y</dt>
<dd>What kind of transformation of the scale to apply.
By default MFI is presented in a "log10" scale. Available options are
described in the documentation of <a href="https://ggplot2.tidyverse.org/reference/scale_continuous.html">scale_y_continuous</a>
under<code>transform</code> parameter.</dd>
<dt>plot_outliers</dt>
<dd>When using "boxplot" type of a plot
one can set this parameter to TRUE and display the names of samples for
which MFI falls outside the 1.5 IQR interval</dd></dl>

Arguments

Plot MFI value distribution for a given analyte — plot_mfi_for_analyte

<dl>

<dt>plate</dt>
<dd>A plate object</dd>


<dt>analyte_name</dt>
<dd>The analyte to plot</dd>


<dt>data_type</dt>
<dd>The type of data to plot. Default is "Median"</dd>


<dt>plot_type</dt>
<dd>The type of plot to generate. Default is "violin".
Available options are "boxplot" and "violin".</dd>


<dt>scale_y</dt>
<dd>What kind of transformation of the scale to apply.
By default MFI is presented in a "log10" scale. Available options are
described in the documentation of <a href='https://ggplot2.tidyverse.org/reference/scale_continuous.html'>scale_y_continuous</a>
under<code>transform</code> parameter.</dd>


<dt>plot_outliers</dt>
<dd>When using "boxplot" type of a plot
one can set this parameter to TRUE and display the names of samples for
which MFI falls outside the 1.5 IQR interval</dd>

</dl>

plot_mfi_for_analyte: Plot MFI value distribution for a given analyte

Description

Usage

Value

Arguments