Mercurial > repos > devteam > dwt_cor_ava_perclass
diff execute_dwt_cor_aVa_perClass.R @ 2:b87bbe6bc044 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
author | devteam |
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date | Mon, 06 Jul 2020 20:28:54 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/execute_dwt_cor_aVa_perClass.R Mon Jul 06 20:28:54 2020 -0400 @@ -0,0 +1,178 @@ +################################################################################## +## code to do all correlation tests of form: motif(a) vs. motif(a) +## add code to create null bands by permuting the original data series +## generate plots and table matrix of correlation coefficients including p-values +################################################################################## +library("wavethresh"); +library("waveslim"); + +options(echo = FALSE) + +## normalize data +norm <- function(data) { + v <- (data - mean(data)) / sd(data); + if (sum(is.na(v)) >= 1) { + v <- data; + } + return(v); +} + +dwt_cor <- function(data_short, names_short, data_long, names_long, test, pdf, table, filter = 4, bc = "symmetric", method = "kendall", wf = "haar", boundary = "reflection") { + print(test); + print(pdf); + print(table); + + pdf(file = pdf); + final_pvalue <- NULL; + title <- NULL; + + short_levels <- wavethresh::wd(data_short[, 1], filter.number = filter, bc = bc)$nlevels; + title <- c("motif"); + for (i in 1:short_levels) { + title <- c(title, paste(i, "cor", sep = "_"), paste(i, "pval", sep = "_")); + } + print(title); + + ## normalize the raw data + data_short <- apply(data_short, 2, norm); + data_long <- apply(data_long, 2, norm); + + for (i in seq_len(length(names_short))) { + ## Kendall Tau + ## DWT wavelet correlation function + ## include significance to compare + wave1_dwt <- NULL; + wave2_dwt <- NULL; + tau_dwt <- NULL; + out <- NULL; + + print(names_short[i]); + print(names_long[i]); + + ## need exit if not comparing motif(a) vs motif(a) + if (names_short[i] != names_long[i]) { + stop(paste("motif", names_short[i], "is not the same as", names_long[i], sep = " ")); + } + else { + wave1_dwt <- waveslim::dwt(data_short[, i], wf = wf, short_levels, boundary = boundary); + wave2_dwt <- waveslim::dwt(data_long[, i], wf = wf, short_levels, boundary = boundary); + tau_dwt <- vector(length = short_levels) + + ## perform cor test on wavelet coefficients per scale + for (level in 1:short_levels) { + w1_level <- NULL; + w2_level <- NULL; + w1_level <- (wave1_dwt[[level]]); + w2_level <- (wave2_dwt[[level]]); + tau_dwt[level] <- cor.test(w1_level, w2_level, method = method)$estimate; + } + + ## CI bands by permutation of time series + feature1 <- NULL; + feature2 <- NULL; + feature1 <- data_short[, i]; + feature2 <- data_long[, i]; + null <- NULL; + results <- NULL; + med <- NULL; + cor_25 <- NULL; + cor_975 <- NULL; + + for (k in 1:1000) { + nk_1 <- NULL; + nk_2 <- NULL; + null_levels <- NULL; + cor <- NULL; + null_wave1 <- NULL; + null_wave2 <- NULL; + + nk_1 <- sample(feature1, length(feature1), replace = FALSE); + nk_2 <- sample(feature2, length(feature2), replace = FALSE); + null_levels <- wavethresh::wd(nk_1, filter.number = filter, bc = bc)$nlevels; + cor <- vector(length = null_levels); + null_wave1 <- waveslim::dwt(nk_1, wf = wf, short_levels, boundary = boundary); + null_wave2 <- waveslim::dwt(nk_2, wf = wf, short_levels, boundary = boundary); + + for (level in 1:null_levels) { + null_level1 <- NULL; + null_level2 <- NULL; + null_level1 <- (null_wave1[[level]]); + null_level2 <- (null_wave2[[level]]); + cor[level] <- cor.test(null_level1, null_level2, method = method)$estimate; + } + null <- rbind(null, cor); + } + + null <- apply(null, 2, sort, na.last = TRUE); + print(paste("NAs", length(which(is.na(null))), sep = " ")); + cor_25 <- null[25, ]; + cor_975 <- null[975, ]; + med <- (apply(null, 2, median, na.rm = TRUE)); + + ## plot + results <- cbind(tau_dwt, cor_25, cor_975); + matplot(results, type = "b", pch = "*", lty = 1, col = c(1, 2, 2), ylim = c(-1, 1), xlab = "Wavelet Scale", ylab = "Wavelet Correlation Kendall's Tau", main = (paste(test, names_short[i], sep = " ")), cex.main = 0.75); + abline(h = 0); + + ## get pvalues by comparison to null distribution + ### modify pval calculation for error type II of T test #### + out <- (names_short[i]); + for (m in seq_len(length(tau_dwt))) { + print(paste("scale", m, sep = " ")); + print(paste("tau", tau_dwt[m], sep = " ")); + print(paste("med", med[m], sep = " ")); + out <- c(out, format(tau_dwt[m], digits = 3)); + pv <- NULL; + if (is.na(tau_dwt[m])) { + pv <- "NA"; + } + else { + if (tau_dwt[m] >= med[m]) { + ## R tail test + print(paste("R")); + ### per sv ok to use inequality not strict + pv <- (length(which(null[, m] >= tau_dwt[m]))) / (length(na.exclude(null[, m]))); + if (tau_dwt[m] == med[m]) { + print("tau == med"); + print(summary(null[, m])); + } + } + else if (tau_dwt[m] < med[m]) { + ## L tail test + print(paste("L")); + pv <- (length(which(null[, m] <= tau_dwt[m]))) / (length(na.exclude(null[, m]))); + } + } + out <- c(out, pv); + print(paste("pval", pv, sep = " ")); + } + final_pvalue <- rbind(final_pvalue, out); + print(out); + } + } + colnames(final_pvalue) <- title; + write.table(final_pvalue, file = table, sep = "\\t", quote = FALSE, row.names = FALSE) + dev.off(); +} +## execute +## read in data +args <- commandArgs(trailingOnly = TRUE) + +input_data1 <- NULL; +input_data2 <- NULL; +input_data_short1 <- NULL; +input_data_short2 <- NULL; +input_data_names_short1 <- NULL; +input_data_names_short2 <- NULL; + +input_data1 <- read.delim(args[1]); +input_data_short1 <- input_data1[, +c(seq_len(ncol(input_data1)))]; +input_data_names_short1 <- colnames(input_data_short1); + +input_data2 <- read.delim(args[2]); +input_data_short2 <- input_data2[, +c(seq_len(ncol(input_data2)))]; +input_data_names_short2 <- colnames(input_data_short2); + +## cor test for motif(a) in input_data1 vs motif(a) in input_data2 +dwt_cor(input_data_short1, input_data_names_short1, input_data_short2, input_data_names_short2, test = "cor_aVa", pdf = args[3], table = args[4]); +print("done with the correlation test");