PhyclusVar: PhyclusVar
In Sautie/MALDITOFSpectraPA: Processing and analysis of MALDI_TOF spectra

builds different types of dendrograms for isolates selected and categorized based on varCat2 and varCat1 levels

PhyclusVar(
  df_m,
  meth = "ward.D2",
  d = "euclidean",
  varCat1,
  value,
  varCat2,
  dendrogram = "phylogram",
  ni = 1,
  nf = 10
)

`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", default value), "euclidean", "maximum", "manhattan", "canberra", "binary" "minkowski"
`varCat1:`	categorical variable, example: "Taxonomie" ,"Genre", "Date.d.analyse" ,"Origine","Ruche", "Nutrition" , "Date.de.récolte" , "Lieu.de.la.ruche"
`value:`	value of catVar1 "Lactobacillus" ("Genre"), Taxonomie("Pediococcus pentosaceus"), "Erica cinerea" ("Nutrition"),...
`varCat2:`	categorical variable
`nc:`	n of clusters (nc=4, default value)
`dendrogram:`	dendrogram type ("phylogram", default value), "cladogram", "unrooted", "fan" and "radial"

output cophenetic coefficient and figure @examples dft<-PhyclusVar(df_Peaks, varCat1="Genre", value="Lactobacillus", varCat2="Nutrition"), dft<-PhyclusVar(df_Peaks, varCat1="Taxonomie", value="Lactobacillus plantarum", varCat2="Ruche") dft<-PhyclusVar(df_Peaks, varCat1="Taxonomie", value="Pediococcus pentosaceus", varCat2="Nutrition", dendrogram="cladogram"), dft<-PhyclusVar(df_Peaks, varCat1="Taxonomie", value="All", varCat2="Date.de.récolte", dendrogram="fan") dft<-PhyclusVar(df_Peaks, varCat1="Taxonomie", value="Lactobacillus plantarum", varCat2="Ruche", dendrogram="fan"), dft<-PhyclusVar(df_Peaks, varCat1="Taxonomie", value="Lactobacillus plantarum", varCat2="Ruche", dendrogram="unrooted") 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.