correlation_analysis: correlation

annotate correlation_analysis.r @ 0:58997c28b268 draft default tip

"planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e"

author	workflow4metabolomics
date	Tue, 19 Jan 2021 16:41:47 +0000
parents
children

rev	line source
0 58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	1 #!/usr/local/public/bin/Rscript --vanilla --slave --no-site-file
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	2 #For questions: Antoine Gravot (Protocole conception) and Misharl Monsoor (for galaxy wrapper and R script).
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	3
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	4 #Load the different libraries
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	5 library(batch) #necessary for parseCommandArgs function
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	6 library(reshape) #necessary for using melt function
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	7 library(MASS) # necessary for using the write.matrix()
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	8 #interpretation of arguments given in command line as an R list of objects
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	9 list_arguments <- parseCommandArgs(evaluate = FALSE)
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	10
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	11 cat("\nJob starting time:\n", format(Sys.time(), "%a %d %b %Y %X"),
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	12 "\n\n--------------------------------------------------------------------",
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	13 "\nParameters used in 'Metabolites Correlation Analysis':\n\n")
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	14 print(list_arguments)
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	15 cat("--------------------------------------------------------------------\n\n")
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	16
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	17 #The main function of this script that will execute all the other functions
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	18
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	19
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	20 main_function <- function(sorting, variable_metadata, data_matrix, sample_metadata, corrdel, param_correlation, param_cytoscape, matrix_corr, user_matrix_corr, corr_method) {
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	21
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	22
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	23 if (sorting == 1) {
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	24 ####Executing the sorting function####
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	25 cat("\nExecuting the sorting function\n")
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	26 #Read the tsv annotateDiffreport file and don't modify the columns name (check.names = FALSE)
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	27 variable_metadata_input <- read.csv(variable_metadata, header = T, sep = "\t", dec = ".", check.names = FALSE)
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	28 data_matrix_input <- read.csv(data_matrix, header = T, sep = "\t", dec = ".", check.names = FALSE)
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	29 first_column_variable <- toString(names(variable_metadata_input)[1])
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	30 first_column_datamatrix <- toString(names(data_matrix_input)[1])
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	31 #@TODO merge
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	32 input_tsv <- cbind(variable_metadata_input, data_matrix_input[, !(colnames(data_matrix_input) %in% c(first_column_datamatrix))])
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	33 #Load the sample.info from the xcmsSet
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	34 sample_metadata_info_tsv <- read.table(sample_metadata, header = T, sep = "\t", dec = ",", check.names = FALSE)
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	35 #Extract the samples name from the sample.info file generated from the xcmsSet step in ABIMS Workflow4Metabo.
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	36 samples_name <- as.vector(t(sample_metadata_info_tsv[1]))
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	37 output_tsv <- sorting(input_tsv, samples_name)
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	38 # output now if corrdel == 0
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	39 if (corrdel == 0) {
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	40 output_tsv_vm <- output_tsv[, which(!(colnames(output_tsv) %in% samples_name))]
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	41 write.table(output_tsv_vm[, c(3:ncol(output_tsv_vm), 2, 1)], sep = "\t", quote = FALSE, col.names = TRUE, row.names = FALSE, file = "sorted_table.tsv")
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	42 }
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	43
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	44 }
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	45 if (corrdel == 1) {
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	46 cat("\nExecuting the corr_matrix_del function\n")
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	47 corr_matrix_del(output_tsv, samples_name, param_correlation, param_cytoscape, corr_method)
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	48 }
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	49
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	50 if (matrix_corr == 1) {
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	51 cat("\nExecuting the corr_matrix function\n")
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	52 corr_matrix_user(user_matrix_corr, param_cytoscape, corr_method)
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	53
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	54 }
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	55
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	56 }
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	57
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	58 #The sorting function will sort the dataframe by rt column.
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	59 #Then it creates a "signal_moy" column which contains the mean values of the signal values of the sample by row.
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	60 #It finally creates a table tsv format "sorted_table.tsv".
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	61
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	62 sorting <- function(input_tsv, samples_name) {
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	63
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	64 #Sort by rt column
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	65 new_input <- input_tsv[order(input_tsv$rt), ]
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	66 #Compute the mean operation of all the signal values of the sample by row, and put the results in a new column "signal_moy"
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	67 new_input["signal_moy"] <- data.frame(Means = rowMeans(new_input[, colnames(new_input) %in% samples_name]))
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	68 #Rearrange the data frame in order to have the columns "signal_moy" and "pcgroup" at the beginning of the table
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	69 new_input <- cbind(new_input["signal_moy"], new_input["pcgroup"], new_input[, !(colnames(new_input) %in% c("signal_moy", "pcgroup"))])
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	70 #Sort the "signal_moy" column data frame by pcgroup
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	71 new_input <- new_input[order(new_input$pcgroup, -new_input$signal_moy), ]
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	72 #Write the data frame to a file named "sorted_table.tsv"
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	73 #Erase the rownames of the table
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	74 rownames(new_input) <- NULL
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	75 #Suppress rows which contains Nas
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	76 new_input <- new_input[complete.cases(new_input$pcgroup), ]
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	77 return(new_input)
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	78 }
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	79
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	80 corr_matrix_del <- function(output_tsv, samples_name, param_correlation, param_cytoscape, corr_method) {
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	81
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	82 #statmatrix, a dataframe which contains only the columns "name" and the values of the intensity for all the samples
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	83 first_column <- toString(names(output_tsv)[3])
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	84 statmatrix <- output_tsv[(names(output_tsv) %in% c(first_column, samples_name))]
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	85 statmatrix2 <- output_tsv[(names(output_tsv) %in% c(first_column, "signal_moy", samples_name))]
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	86 n <- statmatrix[, first_column]
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	87 #transpose all but the first column (name)
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	88 statmatrix <- as.data.frame(t(statmatrix[, -1]))
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	89 #Rename the columns of the dataframe "statmatrix"
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	90 colnames(statmatrix) <- n
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	91 #Transform dataframe to matrix before doing the cor function
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	92 corr_transpo <- data.matrix(statmatrix)
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	93 #Create a matrix which contains only the data of the samples without the other columns
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	94 statmatrix <- output_tsv[(names(output_tsv) %in% c(samples_name))]
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	95 #Add the rownames previously
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	96 rownames(statmatrix) <- make.unique(as.vector(output_tsv[, first_column]))
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	97 #Do the cor step, with the transposed statmatrix (metabolites as columns)
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	98 corr_transpo <- cor(t(as.matrix(statmatrix)), method = corr_method)
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	99 #Add the columns "signal_moy", "pcgroup" and "name" to the final correlation matrix output
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	100 new_dataframe <- cbind(output_tsv["signal_moy"], output_tsv["pcgroup"], output_tsv[names(output_tsv)[3]], corr_transpo)
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	101 #Add a new column "suppress" which indicates if the metabolite will be removed from the analysis (because it is correlated with the other metabolite)
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	102 new_dataframe["suppress"] <- ""
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	103 #Take the pcgroup names
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	104 pcgroups <- unique(new_dataframe$pcgroup)
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	105 #Remove NAs from the pcgroups vector
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	106 pcgroups <- pcgroups[which(pcgroups != "NA")]
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	107 #Creates a pcgroups list
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	108 list_data <- vector(mode = "list", length = length(pcgroups))
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	109 #Will do the following steps by pcgroup
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	110 for (pcgroup in pcgroups) {
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	111 #Select a subset data frame for each pcgroup
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	112 subset_data <- new_dataframe[new_dataframe$pcgroup == pcgroup, ]
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	113 #Stores the metabolites names for each pcgroup into a matrix one dimension.
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	114 pc_group_elements <- t(as.matrix(subset_data[3]))
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	115 #uses the matrix "pc_group_elements" containing the metabolites to have the correlation data frame "subset_data2" by pcgroup
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	116 subset_data2 <- subset_data[names(subset_data) %in% c(names(output_tsv)[3], pc_group_elements)]
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	117 #We keep the first metabolites for each pcgroup that correspond to the metabolites with the highest amount of signal
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	118 first_metabolite <- pc_group_elements[1]
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	119 #Remove the first metabolite from the pc_group_elements matrix
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	120 pc_group_elements <- pc_group_elements[, c(seq_len(length(pc_group_elements)))]
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	121 #print (pc_group_elements)
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	122 for (metabolite in pc_group_elements) {
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	123 metabolite_dataframe <- subset_data2[subset_data2[, first_column] == metabolite, ]
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	124 #retrives metabolite index from the vector object "pc_group_elements"
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	125 index_metabolite <- as.numeric(which(pc_group_elements == metabolite, arr.ind = TRUE))
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	126 for (f in 2:index_metabolite - 1) {
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	127 if (metabolite != first_metabolite) {
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	128 value_intensity <- t(data.matrix(metabolite_dataframe[, pc_group_elements[f]]))
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	129 value_intensity <- value_intensity[1:1]
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	130 #If one value is >0.75, it means that the metabolite est correlated with at least one previous metabolite in the table, so the boolean variable is set to true.
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	131 if (value_intensity > param_correlation) {
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	132 new_dataframe$suppress[new_dataframe[, first_column] == metabolite] <- "DEL"
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	133 }
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	134 }
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	135 }
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	136 }
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	137 }
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	138 #The dataframe with the column "suppress" at the begginning
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	139 new_dataframe_suppression <- cbind(new_dataframe[first_column], new_dataframe["suppress"], output_tsv["rt"], new_dataframe["signal_moy"], new_dataframe[, !(colnames(new_dataframe) %in% c(first_column, "suppress", "pcgroup", "signal_moy"))])
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	140
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	141
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	142 #remove all the rows which have the "suppress" data and keep only the selected metabolites
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	143 selected_metabolite_dataframe <- new_dataframe_suppression[new_dataframe_suppression$suppress != "DEL", ]
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	144 #Keep the metabolites selected in a list
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	145 metabolites_selected_list <- as.vector(t(selected_metabolite_dataframe[1]))
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	146 #Add the other columns to keep
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	147 metabolites_selected_list <- c(metabolites_selected_list, first_column, "rt", "signal_moy")
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	148 #Keep the metabolites selected to keep only the columns
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	149 selected_metabolite_dataframe <- selected_metabolite_dataframe[, colnames(selected_metabolite_dataframe) %in% metabolites_selected_list]
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	150
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	151 #Export to siff table format for visualization in cytoscape for the selected metabolites
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	152 siff_table <- melt(selected_metabolite_dataframe[, !colnames(selected_metabolite_dataframe) %in% c("pcgroup", "rt", "signal_moy")])
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	153 #Remove the values equal to 1 (correlation between two metabolite identical)
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	154 siff_table <- siff_table[siff_table$value != 1, ]
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	155 #Keep only the values corresponding to the param_cytoscape
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	156 siff_table <- siff_table[siff_table$value >= param_cytoscape, ]
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	157 #Change the order of the columns
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	158 siff_table <- cbind(siff_table[first_column], siff_table["value"], siff_table["variable"])
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	159
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	160
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	161
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	162 #Join the two datasets to keep only the selected metabolite, with all the information about the intensity value for statistics analysis in the next step of the workflow.
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	163 joined_dataframe <- merge(statmatrix2, selected_metabolite_dataframe[first_column], by = first_column)
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	164 #Order by the signal intensity
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	165 joined_dataframe <- joined_dataframe[order(-joined_dataframe$signal_moy), ]
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	166 #Transposition of the dataframe
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	167 joined_dataframe <- joined_dataframe[, !(colnames(joined_dataframe) %in% c("signal_moy"))]
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	168
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	169
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	170 #Write the different tables into files
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	171 write.table(selected_metabolite_dataframe, sep = "\t", quote = FALSE, col.names = TRUE, row.names = FALSE, file = "correlation_matrix_selected.tsv")
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	172 write.table(siff_table, sep = "\t", quote = FALSE, col.names = FALSE, row.names = FALSE, file = "siff_table.tsv")
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	173 output_tsv_vm <- output_tsv[, which(!(colnames(output_tsv) %in% samples_name))]
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	174 output_tsv_vm <- data.frame(output_tsv_vm[, c(3:ncol(output_tsv_vm), 2, 1)], ori.or = seq_len(nrow(output_tsv_vm)))
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	175 output_tsv_vm <- merge(x = output_tsv_vm, y = new_dataframe[, c(3, which(colnames(new_dataframe) == "suppress"))], by.x = 1, by.y = 1, sort = FALSE)
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	176 output_tsv_vm <- output_tsv_vm[order(output_tsv_vm$ori.or), ][, -c(which(colnames(output_tsv_vm) == "ori.or"))]
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	177 write.table(output_tsv_vm, sep = "\t", quote = FALSE, col.names = TRUE, row.names = FALSE, file = "sorted_table.tsv")
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	178
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	179 }
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	180
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	181
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	182 corr_matrix_user <- function(user_matrix_corr, param_cytoscape, corr_method) {
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	183 #read the input table
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	184 input_tsv <- read.csv(user_matrix_corr, header = T, sep = "\t", dec = ".", check.names = FALSE)
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	185 n <- input_tsv$HD
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	186 #transpose all but the first column (name)
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	187 statmatrix_corr <- as.data.frame(t(input_tsv[, -1]))
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	188 #Rename the columns of the dataframe "statmatrix"
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	189 colnames(statmatrix_corr) <- n
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	190 #Do the cor step, with the transposed statmatrix.
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	191 corr_transpo <- cor(t(as.matrix(statmatrix_corr)), method = corr_method)
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	192 #Write the matrix to a tsv file
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	193 write.table(corr_transpo, sep <- "\t", quote = FALSE, col.names = NA, file = "correlation_matrix.tsv")
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	194 #Export to siff table format for visualization in cytoscape for the selected conditions
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	195 siff_table <- melt(corr_transpo)
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	196 #Remove the values equal to 1 (correlation between two metabolite identical)
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	197 siff_table <- siff_table[siff_table$value != 1, ]
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	198 #Keep only the values corresponding to the param_cytoscape
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	199 siff_table <- siff_table[siff_table$value >= param_cytoscape, ]
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	200 #Change the order of the columns
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	201 siff_table <- cbind(Node1 = siff_table["X1"], interaction = siff_table["value"], Node2 = siff_table["X2"])
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	202 #Write the siff table
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	203 write.table(siff_table, sep = "\t", quote = FALSE, col.names = FALSE, row.names = FALSE, file = "siff_table.tsv")
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	204
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	205 }
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	206 do.call(main_function, list_arguments)
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	207
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	208
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	209 cat("\n--------------------------------------------------------------------",
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	210 "\nInformation about R (version, Operating System, attached or loaded packages):\n\n")
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	211 sessionInfo()
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	212 cat("--------------------------------------------------------------------\n",
58997c28b268 "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ commit 35a01e4ef59a91f43d0b1de1d08db29dcc7aae1e" workflow4metabolomics parents: diff changeset	213 "\nJob ending time:\n", format(Sys.time(), "%a %d %b %Y %X"))

Mercurial > repos > workflow4metabolomics > correlation_analysis

annotate correlation_analysis.r @ 0:58997c28b268 draft default tip