Phyclus: Phyclus

In Sautie/MALDITOFSpectraPA: Processing and analysis of MALDI_TOF spectra

Description

builds different types of dendrograms for isolates chosen according to varCat1 levels

Usage

Phyclus(
  df_m,
  meth = "ward.D2",
  d = "euclidean",
  varCat1,
  value,
  dendrogram = "phylogram",
  nc = 4,
  ni = 1,
  nf = 10
)

Arguments

ni, nf:	first and last columns corresponding to categorical variables (default values, ni=1, nf=10)
df_m:	dataframe containing peaks and metadata
meth:	hierarchical clustering algorithm ("ward2", default value), other values: "average", "ward.D", "single", "complete", "mcquitty", "median" or "centroid"
dist:	distance ("euclidean", defaul), "euclidean", "maximum", "manhattan", "canberra", "binary" "minkowski"
varCat1:	categorical variable, example: "Genre","Taxonomie", " Nutrition", "Ruche"...
value:	value of catVar1 "Lactobacillus" ("Genre"), Taxonomie("Pediococcus pentosaceus"), "Erica cinerea" ("Nutrition"),...
nc:	n of clusters (nc=4, default)
dendrogram:	dendrogram type ("phylogram", default value), "cladogram", "unrooted", "fan" and "radial"

Value

output cluster and figure

Examples

   c<-Phyclus(df_Peaks, varCat1="Taxonomie",value="Pediococcus pentosaceus"),
             c<-Phyclus(df_Peaks, varCat1="Nutrition",value="Erica cinerea")
             c<-Phyclus(df_Peaks, varCat1="Taxonomie",value="Pediococcus pentosaceus", dendogram="cladogram")
             source: https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/hclust
                     https://www.rdocumentation.org/packages/ape/versions/5.4-1

Sautie/MALDITOFSpectraPA documentation built on Dec. 31, 2020, 4:28 p.m.