PathogenCompositionPsyringaePhylogroups: Compositions of Pseudomonas syringae at the phylogroup...

In StrainRanking: Ranking of Pathogen Strains

Description

Compositions of Pseudomonas syringae formed from samples collected in South-East France, in Lower Durance River valley and in Upper Durance River valley (Monteil et al., 2014).

Usage

data(PathogenCompositionPsyringaePhylogroups)

Format

A data frame with two rows, each row providing the pathogen composition (PC) at a given date (1st row: PC collected in Lower Durance River valley; 2nd row: PC collected in Upper Durance River valley).

References

Monteil C L, Lafolie F, Laurent J, Clement J C, Simler R, Travi Y, Morris C E (2014). Soil water flow is a source of the plant pathogen Pseudomonas syringae in subalpine headwaters. Environ. Microbiol. 16: 203862052.

Soubeyrand S, Garreta V, Monteil C, Suffert F, Goyeau H, Berder J, Moinard J, Fournier E, Tharreau D, Morris C, Sache I (2017). Testing differences between pathogen compositions with small samples and sparse data. Phytopathology 107: 1199-1208. http://doi.org/10.1094/PHYTO-02-17-0070-FI

See Also

PathogenCompositionPsyringaeClades, PathogenCompositionPsyringaeHaplotypes

Examples

## Load Pathogen Compositions of P. syringae at the phylogroup resolution
data(PathogenCompositionPsyringaePhylogroups)

## Size of the first sample
sum(PathogenCompositionPsyringaePhylogroups[1,])

## Size of the second sample
sum(PathogenCompositionPsyringaePhylogroups[2,])

## Total number of different variants
ncol(PathogenCompositionPsyringaePhylogroups)

## Display pathogen compositions
x=PathogenCompositionPsyringaePhylogroups
barplot(t(x), col=rainbow(ncol(x)), main="P. syringae - Phylogroups")

StrainRanking documentation built on May 2, 2019, 3:38 p.m.