# Correction in correlation method in rquery.cormat

This is a new thread since the original post is closed:

The provided solution works if you want to get only the p-values, but it continues to give the default (Pearson correlation) in the "r" matrix. The variable needs to also be changed for the cor() function. Here is the function with the small correction applied (@raytong thanks for providing the original fix, btw!):

``````#The cor.method applies both to the p value and the correlation calculation.
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", method= cor.method, ...),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)
}
``````

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