Correlation method in rquery.cormat

[VonaM]

Dear R-sudio community,
I am working with the workpachage rquery.cormat. By defaut, the correlation method is pearson (I guess), and I want to change because my data are not normal. So, as recommanded I add method = 'spearman', but it does not work. I have a error message telling my the arg should be one of "circle", "square", "ellipse", ...
Can you help me ?
Thanks,

[raytong]

Hi @VonaM. I check the code of rquery.cormat. It combine a number of functions. Your problem due the function called two functions cor.test and corrplot and both functions have method argument. So, you pass method = "spearman" to it for cor.test but function corrplot get the method argument wrongly. I add cor.method argument to cor.test and plot.method argument to corrplot to separate them and never use method argument which will cause error. You can run it by passing the cor.method = "spearman".

library(tidyverse)

rquery.cormat<-function(x, type=c('lower', 'upper', 'full', 'flatten'),
                        graph=TRUE, graphType=c("correlogram", "heatmap"),
                        col=NULL, cor.method = "pearson", plot.method = "circle", ...)
{
  library(corrplot)
  # Helper functions
  #+++++++++++++++++
  # Compute the matrix of correlation p-values
  cor.pmat <- function(x, ...) {
    mat <- as.matrix(x)
    n <- ncol(mat)
    p.mat<- matrix(NA, n, n)
    diag(p.mat) <- 0
    for (i in 1:(n - 1)) {
      for (j in (i + 1):n) {
        tmp <- cor.test(mat[, i], mat[, j], method = cor.method, ...)
        p.mat[i, j] <- p.mat[j, i] <- tmp$p.value
      }
    }
    colnames(p.mat) <- rownames(p.mat) <- colnames(mat)
    p.mat
  }
  # Get lower triangle of the matrix
  getLower.tri<-function(mat){
    upper<-mat
    upper[upper.tri(mat)]<-""
    mat<-as.data.frame(upper)
    mat
  }
  # Get upper triangle of the matrix
  getUpper.tri<-function(mat){
    lt<-mat
    lt[lower.tri(mat)]<-""
    mat<-as.data.frame(lt)
    mat
  }
  # Get flatten matrix
  flattenCorrMatrix <- function(cormat, pmat) {
    ut <- upper.tri(cormat)
    data.frame(
      row = rownames(cormat)[row(cormat)[ut]],
      column = rownames(cormat)[col(cormat)[ut]],
      cor  =(cormat)[ut],
      p = pmat[ut]
    )
  }
  # Define color
  if (is.null(col)) {
    col <- colorRampPalette(c("#67001F", "#B2182B", "#D6604D", 
                              "#F4A582", "#FDDBC7", "#FFFFFF", "#D1E5F0", "#92C5DE", 
                              "#4393C3", "#2166AC", "#053061"))(200)
    col<-rev(col)
  }
  
  # Correlation matrix
  cormat<-signif(cor(x, use = "complete.obs", ...),2)
  pmat<-signif(cor.pmat(x, ...),2)
  # Reorder correlation matrix
  ord<-corrMatOrder(cormat, order="hclust")
  cormat<-cormat[ord, ord]
  pmat<-pmat[ord, ord]
  # Replace correlation coeff by symbols
  sym<-symnum(cormat, abbr.colnames=FALSE)
  # Correlogram
  if(graph & graphType[1]=="correlogram"){
    corrplot(cormat, type=ifelse(type[1]=="flatten", "lower", type[1]),
             tl.col="black", tl.srt=45,col=col, method = plot.method, ...)
  }
  else if(graphType[1]=="heatmap")
    heatmap(cormat, col=col, symm=TRUE)
  # Get lower/upper triangle
  if(type[1]=="lower"){
    cormat<-getLower.tri(cormat)
    pmat<-getLower.tri(pmat)
  }
  else if(type[1]=="upper"){
    cormat<-getUpper.tri(cormat)
    pmat<-getUpper.tri(pmat)
    sym=t(sym)
  }
  else if(type[1]=="flatten"){
    cormat<-flattenCorrMatrix(cormat, pmat)
    pmat=NULL
    sym=NULL
  }
  list(r=cormat, p=pmat, sym=sym)
}

1:10 %>%
  matrix(ncol = 2) %>%
  rquery.cormat(cor.method = "spearman", plot.method = "circle")
#> corrplot 0.84 loaded

#> $r
#>   V1 V2
#> 1  1   
#> 2  1  1
#> 
#> $p
#>      V1 V2
#> 1     0   
#> 2 0.017  0
#> 
#> $sym
#>         
#> [1,] 1  
#> [2,] 1 1
#> attr(,"legend")
#> [1] 0 ' ' 0.3 '.' 0.6 ',' 0.8 '+' 0.9 '*' 0.95 'B' 1

^{Created on 2019-10-24 by the reprex package (v0.3.0)}