popsWithin

Helper that will be used by popsCompute to determine which objects are within populations or not.

internal

Contains several tools to treat imaging flow cytometry data from 'ImageStream®' and 'FlowSight®' cytometers ('Amnis®' 'Cytek®'). Provides an easy and simple way to read and write .fcs, .rif, .cif and .daf files. Information such as masks, features, regions and populations set within these files can be retrieved for each single cell. In addition, raw data such as images stored can also be accessed. Users, may hopefully increase their productivity thanks to dedicated functions to extract, visualize, manipulate and export 'IFC' data. Toy data example can be installed through the 'IFCdata' package of approximately 32 MB, which is available in a 'drat' repository <https://gitdemont.github.io/IFCdata/>. See file 'COPYRIGHTS' and file 'AUTHORS' for a list of copyright holders and authors.

Yohann Demont

Tools for Imaging Flow Cytometry

Gautier Stoll

Guido Kroemer

Jean-Pierre Marolleau

Loïc Garçon

popsWithin function

<dl><dt>pops</dt>
<dd>list of populations.</dd>
<dt>regions</dt>
<dd>list of regions.</dd>
<dt>features</dt>
<dd>dataframe of features.</dd>
<dt>pnt_in_poly_algorithm</dt>
<dd>algorithm used to determine if object belongs to a polygon region or not. Default is 1. 
Note that for the moment only 1(Trigonometry) is available.</dd>
<dt>pnt_in_poly_epsilon</dt>
<dd>epsilon to determine if object belongs to a polygon region or not. It only applies when algorithm is 1. Default is 1e-12.</dd>
<dt>display_progress</dt>
<dd>whether to display a progress bar. Default is TRUE.</dd>
<dt>title_progress</dt>
<dd>character string, giving the title of the progress bar. Default is "".</dd>
<dt>...</dt>
<dd>other arguments to be passed.</dd></dl>

Arguments

IFC_pops Checker for Object Membership to Populations — popsWithin

<dl>

<dt>pops</dt>
<dd>list of populations.</dd>


<dt>regions</dt>
<dd>list of regions.</dd>


<dt>features</dt>
<dd>dataframe of features.</dd>


<dt>pnt_in_poly_algorithm</dt>
<dd>algorithm used to determine if object belongs to a polygon region or not. Default is 1. 
Note that for the moment only 1(Trigonometry) is available.</dd>


<dt>pnt_in_poly_epsilon</dt>
<dd>epsilon to determine if object belongs to a polygon region or not. It only applies when algorithm is 1. Default is 1e-12.</dd>


<dt>display_progress</dt>
<dd>whether to display a progress bar. Default is TRUE.</dd>


<dt>title_progress</dt>
<dd>character string, giving the title of the progress bar. Default is "".</dd>


<dt>...</dt>
<dd>other arguments to be passed.</dd>

</dl>

popsWithin: IFC_pops Checker for Object Membership to Populations

Description

Usage

Arguments