flowDiv: Cytometric Diversity Indices from Gated Data

Description Usage Arguments Value Author(s) References Examples

View source: R/flowDiv_main.R

Description

Uses multidimensional contingency tables to calculate ecological diversity indices from gated populations.

Usage

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flowDiv(myworkspaces, gate.name=NULL, ialpha="invsimpson", ibeta="bray", do.plot=FALSE,

static=FALSE, dilutions=NULL,  pmax=0.05, env=NULL, use.beads=FALSE, beads=NULL,

transform.hell=FALSE, dimension=20, psize=3, autotrans=FALSE)

Arguments

myworkspaces

A list containing the paths to FlowJo workspaces or GatingSet which are meant to be analyzed. More than one workspace can be analyzed at the same time. Workspaces should contain .fcs files (versions 2.0 or 3.0) with its original names.

gate.name

Name of the gate to be analyzed. Must be a single-valued string. The gate should be named exactly the same in all samples from the workspaces.

ialpha

Method used to calculate alpha diversity index of cytograms (i.e. the degree of similarity between two cytograms). Should be one of "shannon", "simpson" or "invsimpson", as for vegan::diversity function. Default is "invsimpson".

ibeta

Method used to calculate beta diversity index of cytograms. Should be one of the sixteeen avaiable for vegan::vegdist function. Default is <e2><80><9c>bray<e2><80><9d>.

do.plot

Logical. It plots scatterplots of gated populations and displays grid lines corresponding to the limits of the bins.

static

Logical. If TRUE, one must set minimum and maximum range for each channel individually.

dilutions

A vector containing dilution factors for each sample in the workspaces. Its lenght is the same as the total number of samples meant to be analyzed and must follow the exact same order in which samples are presented to the function (the order of samples corresponds both to the order of workspace described in "myworkspaces" parameter and their order in each of these FlowJo workspaces). By default, it is assumed that all samples have no dilutions whatsoever (i.e. all dilutions factors equal 1).

pmax

Maximum estimated p value for displayed variables on NMDS plot, as required by vegan::plot.envifit

env

Enviromental matrix associated to the set of cytograms under analysis.

use.beads

Logical. If <e2><80><9c>TRUE<e2><80><9d> , it centers all cytograms under a common point, based on the arithmetic mean of a standard region for all cytograms (usually beads regions), before proceeding to analysis. It is recommended to proceed this way only if samples were analyzed with different settings.

beads

Name of the gate describing the standard region to be used (usually bead's regions). Necessary only if use.beads is set to <e2><80><9c>TRUE<e2><80><9d>. The beads gate should be named exactly the same in all samples from the workspaces.

transform.hell

Logical. If TRUE, Hellinger transformation is applyed to data before analysis.

dimension

Dimensions of plot devices, in centimeters.

psize

Defines the plotting size of bins.

autotrans

Logical. Argument to be passed to vegan::metaMDS function.

Value

A list containing alpha index, beta matrix and Pielou's indices for each cytogram.

Author(s)

Bruno M.S. Wanderley, Maria Victoria Quiroga, Andre M. Amado, Fernando Unrein

References

Li, W.K.W. (1997). Cytometric diversity in marine ultraphytoplankton. Limnology and Oceanography 42, 874<e2><80><93>880.

Examples

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## Not run: 


# Analyzing a .xml FlowJo workspace.

indexes <- flowDiv(myworkspaces = <e2><80><9c>my_workspace.xml<e2><80><9d>,gate.name = <e2><80><9c>my_gate_name<e2><80><9d>)
#assume that the FlowJo workspace is below the current directory



## End(Not run)

bmsw/flowDiv documentation built on May 6, 2019, 9:52 a.m.