Dendrogram_pairComp: Dendrogram_pairComp

In Sautie/MALDITOFSpectraPA: Processing and analysis of MALDI_TOF spectra

Description

Dendrogram_pairComp makes pairwise dendrogram comparisons and correlations

Usage

Dendrogram_pairComp(
  df_m,
  varCat1,
  value,
  methCorr = "cophenetic",
  meth1 = "ward.D2",
  meth2 = "mcquitty",
  meth3 = "complete",
  meth4 = "centroid",
  meth5 = "single",
  meth6 = "average",
  dist1 = "euclidean",
  dist2 = "euclidean",
  dist3 = "euclidean",
  dist4 = "euclidean",
  dist5 = "euclidean",
  dist6 = "euclidean",
  graph = "Complex",
  nc = 3
)

Arguments

meth1, meth2...meth6:	hierarchical clustering algorithms "ward2" ,"average", "ward.D", "single", "complete", "mcquitty", "median" or "centroid"
dist1, dist2, ...dist6:	distances "euclidean", "maximum", "manhattan", "canberra", "binary" "minkowski"
df_m:	dataframe containing peaks and metadata
methCorr:	dendrogram correlation method ("cophenetic", default value), others: "baker", "common_nodes", "FM_index"
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"),...

Value

untangled and tangled dendrograms, dendrogram correlation matrix and statistics @examples mc<-Dendrogram_pairComp(df_Peaks, varCat1="Taxonomie", value="Pediococcus pentosaceus"), mc<-Dendrogram_pairComp(df_Peaks, varCat1="Nutrition", value="Marrubium vulgare") source: https://cran.r-project.org/web/packages/dendextend/vignettes/dendextend.html#:~:text=The https://www.rdocumentation.org/packages/dendextend/versions/1.14.0 https://www.r-graph-gallery.com/340-custom-your-dendrogram-with-dendextend.html https://academic.oup.com/bioinformatics/article/31/22/3718/240978 https://cran.rstudio.com/web/packages/dendextend/vignettes/Cluster_Analysis.html https://www.datanovia.com/en/lessons/comparing-cluster-dendrograms-in-r/ https://rdrr.io/cran/dendextend/man/untangle.html

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