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

Description Usage Arguments Value Examples

Visual_CorrDistM is based on functions for computing and visualizing distance matrix and correlograms

Visual_CorrDistM(
  df_m,
  varCat1,
  value,
  VisualM = "Corr",
  dist = "euclidean",
  Ls = 6,
  CorrFig = "color",
  layout = "upper",
  ord = "FPC",
  pv = TRUE,
  sig = 0.05
)

`df_m:`	dataframe containing peaks and metadata
`dist:`	distances "euclidean", (default value), "euclidean", "maximum", "manhattan", "canberra", "binary", "minkowski", "pearson", "spearman" or "kendall".
`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"),...
`Visual:`	correlogram "Corr", (default value) or distance matrix figure ("Dist") (this second option is more general because it includes correlation, see dist argument)
`CorrFig:`	correlogram type, "circle" , "square", "ellipse", "number", "pie", "shade" and "color" (default value)
`Ord:`	correlogram arrangement methods to find patterns (ord="FPC", default value), "AOE" ,"hclust"
`layout:`	correlogram layout: "full" "upper" "lower", (layout="upper", default value)
`pv:`	boolean variable (including or not probability values) (pv=TRUE, default value)
`sig:`	significance level (sig="0.05", default value)

figures and statistics

     Visual_CorrDistM (df_Peaks, varCat1="Taxonomie", value="Pediococcus pentosaceus"),
               Visual_CorrDistM (df_Peaks, varCat1="Taxonomie", value="Pediococcus pentosaceus", VisualM="dist")
               Visual_CorrDistM (df_Peaks, varCat1="Taxonomie", value="Pediococcus pentosaceus", VisualM="dist", dist="pearson")
        source: https://cran.r-project.org/web/packages/corrplot/vignettes/corrplot-intro.html
                https://www.rdocumentation.org/packages/corrplot/versions/0.84/topics/corrplot