Mercurial > repos > melpetera > corr_table
diff CorrTable/Corr_Script_samples_row.R @ 2:2173ad5e7750 draft default tip
Uploaded
author | melpetera |
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date | Wed, 16 Oct 2019 03:12:55 -0400 |
parents | 29ec7e3afdd4 |
children |
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--- a/CorrTable/Corr_Script_samples_row.R Thu Aug 01 11:30:58 2019 -0400 +++ b/CorrTable/Corr_Script_samples_row.R Wed Oct 16 03:12:55 2019 -0400 @@ -254,23 +254,23 @@ if (test.corr == "yes"){ - pvalue <- vector() - for (i in 1:dim(tab.corr)[1]){ - for (j in 1:dim(tab.corr)[2]){ - suppressWarnings(corrtest <- cor.test(tab2[,i], tab1[,j], method = corr.method)) - pvalue <- c(pvalue, corrtest$p.value) - if (multi.name == "none"){ - if (corrtest$p.value > alpha){ - tab.corr[i,j] <- 0 - } - } - } - } - + repcorrtest1 <- function(vari1,vari2,corrmeth){ + suppressWarnings(corrtest <- cor.test(vari2, vari1, method = corrmeth)) + return(corrtest$p.value) + } + repcorrtest2 <- function(stab,ftab,cormeth){ + listp <- apply(X=ftab,2,repcorrtest1,vari2=stab,corrmeth=cormeth) + return(listp) + } + pvalue <- apply(X=tab1,2,repcorrtest2,ftab=tab2,cormeth=corr.method) + + if(multi.name != "none"){ - adjust <- matrix(p.adjust(pvalue, method = multi.name), nrow = dim(tab.corr)[1], ncol = dim(tab.corr)[2], byrow = T) - tab.corr[adjust > alpha] <- 0 - } + pvalue <- matrix(p.adjust(pvalue, method = multi.name), nrow = dim(tab.corr)[1], ncol = dim(tab.corr)[2]) + } + + tab.corr[pvalue > alpha] <- 0 + } @@ -416,17 +416,14 @@ } # Assign an interval to each correlation coefficient - for (i in 1:dim(melted.tab.corr)[1]){ for (j in 1:(length(cl))){ if (vect[j] == -1){ - melted$classe[i][melted$value[i] >= vect[j] - && melted$value[i] <= vect[j+1]] <- cl[j] + melted$classe[melted$value >= vect[j] & melted$value <= vect[j+1]] <- cl[j] } else { - melted$classe[i][melted$value[i] > vect[j] - && melted$value[i] <= vect[j+1]] <- cl[j] + melted$classe[melted$value > vect[j] & melted$value <= vect[j+1]] <- cl[j] } } - } + # Find the 0 and assign it the white as name if (length(which(vect == 0)) == 1) { @@ -493,5 +490,5 @@ # Function call # correlation.tab(tab1.name, tab2.name, param1.samples, param2.samples, corr.method, test.corr, alpha, multi.name, filter, - # filters.choice, threshold, reorder.var, color.heatmap, type.classes, + # filters.choice, threshold, reorder.var, plot.choice, color.heatmap, type.classes, # reg.value, irreg.vect, output1, output2)