SMDS: SMDS

In Sautie/MALDITOFSpectraPA: Processing and analysis of MALDI_TOF spectra

Description

function for Multidimensional scaling and external cluster-based analysis of Maldi_Tof spectra

Usage

SMDS(df_m, varCat1, value, varCat2, dist = "euclidean", grah = "lab_mdsGroups")

Arguments

df_m:	dataframe containing peaks and metadata
dist:	distances: "euclidean" (default value), "maximum", "manhattan", "canberra", "binary" or "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 the chosen categorical variable catVar1, examples: "Lactobacillus" ("Genre"), Taxonomie("Pediococcus pentosaceus"), "Erica cinerea" ("Nutrition"),...
grah:	graphs: "lab_mdsGroups" (default value), "mdsGroups"

Value

figures and statistics

Examples

SMDS(df_Peaks, varCat1="Genre", value="Lactobacillus",  varCat2="Ruche",dist="euclidean",  grah="lab_mdsGroups")
          SMDS(df_Peaks, varCat1="Genre", value="Lactobacillus" varCat2="Ruche",)
          SMDS(df_Peaks, varCat1="Genre", value="Lactobacillus", varCat2="Nutrition")
          SMDS(df_Peaks, varCat1="Genre", value="All",varCat2="Taxonomie")

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