nmds: NMDS plot of cell numbers

In flowCyBar: Analyze flow cytometric data using gate information

Description

NMDS plot of the relative/percental or normalized cell numbers.

Usage

## S4 method for signature 'data.frame'
nmds(x,distance="bray",autotransform=FALSE,zerodist="add",group,main="",type="p",
cex=0.6,pos=4,shrink=TRUE,legend_pos="topleft",pch=1,col="black",abiotic,p.max=0.05,col_abiotic="magenta",verbose=FALSE,...)

## S4 method for signature 'matrix'
nmds(x,distance="bray",autotransform=FALSE,zerodist="add",group,main="",type="p",
cex=0.6,pos=4,shrink=TRUE,legend_pos="topleft",pch=1,col="black",abiotic,p.max=0.05,col_abiotic="magenta",verbose=FALSE,...)

Arguments

x	Data frame or matrix of relative/percental cell numbers or normalized cell numbers. Use one row per sample and one column per gate. Use the first column for the first gate. The names of the gates may not contain any whitespace. If the values contain commas they must be expressed as ".". Missing values or NA's are not allowed.
distance	Dissimilarity index used in vegdist (default="bray"). For more details type "?metaMDS" into R command line.
autotransform	logical (default=FALSE). Determine the use of simple heuristics for a possible data transformation of typical community data. For more details type "?metaMDS" into R command line.
zerodist	Handling of zero dissimilarities (default="add"). For more details type "?metaMDS" into R command line.)
group	Table with group assignments. Use only one column. Use the first line as header. Assign the samples to groups in the next lines. The order and the number of these lines has to be identical to the order and the number of the samples printed in R. Use only integer values in the range from 1 to 25.
main	Character string used as title of the NMDS plot (default="")
type	Type of the plot (default="p"). The "p" indicates points. For more details type "?points" into R command line.
cex	numeric (default=0.6). Character expansion factor. Used for the final size of the characters.
pos	Position of the text (default=4). Values of 1, 2, 3 and 4 indicate positions below, to the left of, above and to the right of the specified coordinates, respectively.
shrink	logical (default=TRUE). Shrink back species scores if they were expanded originally.
legend_pos	Position of the legend (default="topleft"). For more details type "?legend" into R command line.
pch	Plotting symbol (default=1) if group is FALSE. For more details type "?points" into R command line.
col	Color of the symbols and lines within the plot (default="black") if group is FALSE . Can be a color code or a name.
abiotic	Table with abiotic data. Should be a tab-delimited text file using '.' as decimal delimiter. Use one row for one sample and one column for one abiotic parameter. Use the first column for the first parameter and the first line as header. The order and the number of the lines have to be identical to the order and the number of the samples printed in R.
p.max	Decimal number defining the significance level of the abiotic parameters (default=0.05) if abiotic=TRUE. Only parameters less/equal this value are plotted.
col_abiotic	Color used for the plotted abiotic parameters (default="magenta").
verbose	logical (default=FALSE). Change to TRUE to print results of the metaMDS function and the p-values of the abiotic parameters.
...	Additional parameters used for the plot and the metaMDS function. For more details type "?plot", "?points", "?text" or "?metaMDS" into R command line.

Details

Visualizes the distance between samples based on their cytometrically measured cell abundance information using nonmetric multidimensional scaling (NMDS). NMDS is a mathematical technique to visualize the distances between objects (the samples, in this case). The distances within the plot are used to be in accordance with the dis-/similarities of the samples. The NMDS plot can be created using either the relative/percental cell numbers or the normalized values. If there are high abundance and low abundance gates the NMDS plot could be distorted. In this case it is better to use the normalized values. See reference Koch et al. 2013, Box 1 for more details. The NMDS analysis is performed by using the metaMDS function of the R package "vegan" (see reference Warnes et al. 2013).

Author(s)

Joachim Schumann [e-mail], Christin Koch [e-mail], Susanne G<c3><bc>nther [e-mail], Ingo Fetzer [e-mail], Susann M<c3><bc>ller [e-mail]

References

Koch, Christin and G<c3><bc>nther, Susanne and Desta, Adey Feleke and H<c3><bc>bschmann, Thomas and M<c3><bc>ller, Susann (2013). Cytometric fingerprinting for analysing microbial intra-community structure variation and identifying sub-community function. Nature Protocols, 8(1):190-202,

Gregory R. Warnes, Ben Bolker, Lodewijk Bonebakker, Robert Gentleman, Wolfgang Huber Andy Liaw, Thomas Lumley, Martin Maechler, Arni Magnusson, Steffen Moeller, Marc Schwartz and Bill Venables (2013). gplots: Various R programming tools for plotting data. R package version 2.12.1. http://CRAN.R-project.org/package=gplots

Examples

require(vegan)


## Show the NMDS plot of the normalized cell numbers

data(Cell_number_sample)
Normalized_mean<-normalize(Cell_number_sample[,-1],digits=2)
Normalized_mean<-data.frame(data.matrix(Normalized_mean))
nmds(Normalized_mean)

## Change the title of the plot to "NMDS normalized", use triangles as plotting 
## symbols, change the color to red and position the text below the triangles
## Use a dotted line (lty=3)

data(Cell_number_sample)
Normalized_mean<-normalize(Cell_number_sample[,-1],digits=2)
Normalized_mean<-data.frame(data.matrix(Normalized_mean))
nmds(Normalized_mean,main="NMDS normalized",type="b",pos=1,pch=2,col="red",lty=3)

## Plot sample groups saved as data frame groups
## Print additional information

data(Cell_number_sample)
Normalized_mean<-normalize(Cell_number_sample[,-1],digits=2)
Normalized_mean<-data.frame(data.matrix(Normalized_mean))
groups<-data.frame("groups"=c(1,1,1,1,2,3,3,3,3,3))
nmds(Normalized_mean,group=groups,main="NMDS normalized",verbose=TRUE)

## Plot additional gate information and
## abiotic parameters saved in dataset Abiotic_data_sample

data(Cell_number_sample)
Normalized_mean<-normalize(Cell_number_sample[,-1],digits=2)
Normalized_mean<-data.frame(data.matrix(Normalized_mean))
groups<-data.frame("groups"=c(1,1,1,1,2,3,3,3,3,3))
data(Abiotic_data_sample)
nmds(Normalized_mean,group=groups,main="NMDS normalized",
abiotic=Abiotic_data_sample[,-1],verbose=TRUE)

flowCyBar documentation built on Nov. 8, 2020, 6:59 p.m.