Mercurial > repos > devteam > dwt_cor_avb_all
view execute_dwt_cor_aVb_all.R @ 2:e01e8a9a82f4 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_avb_all commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
author | devteam |
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date | Mon, 06 Jul 2020 20:31:38 -0400 |
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################################################################################# ## code to do all correlation tests of form: motif(a) vs. motif(b) ## 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)$nlevels; title <- c("motif1", "motif2"); for (i in 1:short_levels) { title <- c(title, paste(i, "cor", sep = "_"), paste(i, "pval", sep = "_")); } print(title); ## normalize the raw data data_short <- apply(data_short, 2, norm); data_long <- apply(data_long, 2, norm); ## loop to compare a vs b for (i in seq_len(length(names_short))) { for (j in seq_len(i - 1)) { ## Kendall Tau ## DWT wavelet correlation function ## include significance to compare wave1_dwt <- NULL; wave2_dwt <- NULL; tau_dwt <- NULL; out <- NULL; print(names_short[i]); print(names_long[j]); ## need exit if not comparing motif(a) vs motif(a) if (names_short[i] == names_long[j]) { stop(paste("motif", names_short[i], "is the same as", names_long[j], sep = " ")); } else { wave1_dwt <- waveslim::dwt(data_short[, i], wf = wf, short_levels, boundary = boundary); wave2_dwt <- waveslim::dwt(data_long[, j], wf = wf, short_levels, boundary = boundary); tau_dwt <- vector(length = short_levels) ## perform cor test on wavelet coefficients per scale for (level in 1:short_levels) { w1_level <- NULL; w2_level <- NULL; w1_level <- (wave1_dwt[[level]]); w2_level <- (wave2_dwt[[level]]); tau_dwt[level] <- cor.test(w1_level, w2_level, method = method)$estimate; } ## CI bands by permutation of time series feature1 <- NULL; feature2 <- NULL; feature1 <- data_short[, i]; feature2 <- data_long[, j]; 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); 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], "vs.", names_long[j], 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 <- c(names_short[i], names_long[j]); for (m in seq_len(length(tau_dwt))) { print(m); print(tau_dwt[m]); 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 pv <- (length(which(null[, m] >= tau_dwt[m]))) / (length(na.exclude(null[, m]))); } else { if (tau_dwt[m] < med[m]) { ## L tail test pv <- (length(which(null[, m] <= tau_dwt[m]))) / (length(na.exclude(null[, m]))); } } } out <- c(out, pv); print(pv); } 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(b) in input_data2 dwt_cor(input_data_short1, input_data_names_short1, input_data_short2, input_data_names_short2, test = "cor_aVb_all", pdf = args[3], table = args[4]); print("done with the correlation test");