Vizclus: Vizclus

In Sautie/MALDITOFSpectraPA: Processing and analysis of MALDI_TOF spectra

Description

clusters and builds dendrograms for isolates selected according to varCat1 levels

Usage

Vizclus(
  df_m,
  meth = "ward.D2",
  dist = "euclidean",
  varCat1,
  value,
  nc = 4,
  graph = "phylogram",
  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", default value), "euclidean", "maximum", "manhattan", "canberra", "binary" "minkowski"
varCat1:	categorical variable for choosing isolates, examples: "Taxonomie" ,"Genre", "Date.d.analyse" ,"Origine","Ruche", "Nutrition" , "Date.de.récolte" , "Lieu.de.la.ruche"
value:	level of catVar1, examples, "Lactobacillus" ("Genre"), Taxonomie("Pediococcus pentosaceus"), "Erica cinerea" ("Nutrition"),...
nc:	n of clusters (nc=4, default value)
dendrogram:	dendrogram and factor map

Value

output figures and statistics @examples Lt<-Vizclus(df_Peaks,varCat1="Taxonomie", value="Pediococcus pentosaceus"), Lt<-Vizclus(df_Peaks,varCat1="Ruche", value="VI") Lt<-Vizclus(df_Peaks,varCat1="Nutrition", value="Caraway", nc=2), Lt<-Vizclus(df_Peaks,varCat1="Genre", value="Lactobacillus", nc=4) Lt<-Vizclus(df_Peaks,varCat1="Nutrition", value="All"), Lt<-Vizclus(df_Peaks,varCat1="Nutrition", value="Caraway", nc=3, graph="fm") source: https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/hclust https://www.rdocumentation.org/packages/factoextra/versions/1.0.7/topics/fviz http://www.sthda.com/english/wiki/factoextra-r-package-easy-multivariate-data-analyses-and-elegant-visualization#:~:text=factoextra http://www.sthda.com/english/wiki/beautiful-dendrogram-visualizations-in-r-5-must-known-methods-unsupervised-machine-learning

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