w4mconcatenate: concatenation.R annotate

annotate concatenation.R @ 0:c577f13705f2 draft default tip

planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec

author	workflow4metabolomics
date	Wed, 10 Jul 2024 15:20:11 +0000
parents
children

rev	line source
0 c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	1 if (FALSE) {
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	2 rm(list = ls())
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	3
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	4 DM1 <- data.frame(data = c("5d_-kkcùf", "npèt", "5PY4(*3"),
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	5 `j 785` = c(0.356426723610756, 0.801750949101246, 0.875199970420953),
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	6 `y54j 68y4j6` = c(0.380152310071702, 0.535593104115636, 0.0825428101366147),
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	7 `5-6 4` = c(0.0306944207412024, 0.258351312473067, 0.253659010703906),
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	8 hrrrrh = c(0.334137638848017, 0.599475573145688, 0.507762246807195),
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	9 `5h -` = c(0.298147485608469, 0.0763319665667417, 0.856444177031262))
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	10
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	11 DM2 <- data.frame(data = c("5d_-kkcùf", "npèt", "5PY4(*3"),
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	12 `j 785` = c(0.356426723610756, 0.801750949101246, 0.875199970420953),
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	13 `y54j 68y4j6` = c(0.380152310071702, 0.535593104115636, 0.0825428101366147),
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	14 `5-6 4` = c(0.0306944207412024, 0.258351312473067, 0.253659010703906),
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	15 hrrrrh = c(0.334137638848017, 0.599475573145688, 0.507762246807195),
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	16 `5h -` = c(0.298147485608469, 0.0763319665667417, 0.856444177031262))
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	17
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	18 M1 <- data.frame(samplename = c("j 785", "y54j 68y4j6", "5-6 4", "hrrrrh", "5h -"),
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	19 ABD = c(19, 24, 2, 3, "y"), E = c(9, "p0", 45, 24, 29),
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	20 AAA = c("r", "bg", "il", "d", "b"),
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	21 fp = c("pj", "z", "e", "r", "t"),
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	22 uv = c("s", "d", "f", "s", "d"))
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	23
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	24 M2 <- data.frame(samplename = c("j 785", "y54j 68y4j6", "5-6 4", "hrrrrh", "5h -"),
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	25 ABD = c(19, 24, 2, 3, "y"), E = c(9, "ici", 45, 24, 29),
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	26 AAA = c("r", "bg", "il", "d", "b"),
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	27 fp = c("pj", "z", "e", "r", "t"),
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	28 uv = c("s", "d", "f", "s", "d"))
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	29 type <- "sample"
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	30 concatenation <- "unique"
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	31 tab1 <- "tab1"
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	32 tab2 <- "tab2"
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	33 choice_keep <- "oui"
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	34 keep <- 0
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	35 concat(DM1, M1, DM2, M2, type, tab1, tab2, concatenation, choice_keep, keep)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	36 }
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	37
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	38 #################################################################################################################
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	39
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	40
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	41 concat <- function(DM1, M1, DM2, M2, type, tab1, tab2, concatenation, choice_keep, keep) {
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	42
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	43
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	44
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	45 #DM1/DM2 = data.frame containing data Matrix
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	46 #M1/M2 = data.frame containing sample Metadata or variable Metadata
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	47 #type = "sample" or "variable" depending on Metadata content
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	48 #tab1/tab2 = Suffix for Metadata 1/2
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	49 #concatenation = type of concatenation
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	50 #choice_keep = choice of keeping columns with the same no or keeping just one
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	51 #keep = keep the column in M1 or M2
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	52 #returns the concatenated metadata and the two Data Matrix
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	53
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	54 identifiers_1 <- colnames(M1)[1]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	55 identifiers_2 <- colnames(M2)[1]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	56
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	57 err.stock <- NULL
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	58
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	59 #Concatenation------------------------------------------------------------------
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	60
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	61 #If Metadatas is Sample_Metadata we transpose
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	62 if (type == "sample") {
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	63
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	64 rownames(DM1) <- DM1[, 1]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	65 corner_DM1 <- colnames(DM1)[1]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	66 DM1 <- DM1[, -1, drop = FALSE]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	67 DM1 <- t(DM1)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	68 DM1 <- data.frame(sample = row.names(DM1), DM1, check.names = FALSE)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	69 rownames(DM1) <- NULL
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	70
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	71 rownames(DM2) <- DM2[, 1]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	72 corner_DM2 <- colnames(DM2)[1]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	73 DM2 <- DM2[, -1, drop = FALSE]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	74 DM2 <- t(DM2)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	75 DM2 <- data.frame(sample = row.names(DM2), DM2, check.names = FALSE)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	76 rownames(DM2) <- NULL
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	77 }
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	78
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	79 #Add order of sample and Sort by order
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	80
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	81
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	82 M1$order1 <- seq(1, nrow(M1))
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	83 M2$order2 <- seq(nrow(M1) + 1, nrow(M2) + nrow(M1))
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	84
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	85 M1_bf <- M1[order(M1[, 1]), ]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	86 M2_bf <- M2[order(M2[, 1]), ]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	87
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	88
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	89 #Check the variables in common and extract them.
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	90
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	91
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	92 same <- check_features(M1_bf, M2_bf)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	93 same <- same[- which(same == identifiers_1)]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	94
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	95 #Check that shared variables have the same values.
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	96 #If not, they are renamed or deleted according to the parameters chosen by the user.
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	97 result2 <- compare_same_columns(M1_bf, M2_bf, same, choice_keep, keep, tab1, tab2)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	98 M1 <- result2$M1
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	99 M2 <- result2$M2
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	100
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	101 #Unique--------------------------------------------------------------------------
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	102 if (concatenation == "unique") {
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	103 #Table match check
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	104 #We verify that the individuals are all the same
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	105 err.stock <- match2_bis(M1, M2, type)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	106 check_err(err.stock)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	107 M_merge <- merge(M1, M2, by = 1)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	108 }
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	109
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	110
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	111 #Intersection--------------------------------------------------------------------
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	112
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	113 if (concatenation == "intersection") {
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	114
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	115 #select individuals in common
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	116 sample_common <- intersect(M1[, 1], M2[, 1])
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	117
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	118 #if the list of individuals in common is null, an error message is sent
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	119 if (length(sample_common) == 0) {
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	120 err.stock <- c(err.stock, "\nThere are no individuals in common \n")
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	121 check_err(err.stock)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	122 }
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	123 #if the list of individuals in common is less than 5, then a Warning message is sent
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	124 if (length(sample_common) < 5) {
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	125 cat("\nWarning: Less than 5 individuals in common\n")
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	126 }
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	127 M_merge <- merge(M1, M2, by = 1)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	128 }
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	129
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	130 #Union --------------------------------------------------------------------------
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	131 if (concatenation == "union") {
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	132
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	133 #select common ids
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	134 id_common <- intersect(M1[, 1], M2[, 1])
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	135
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	136 if (is.null(id_common)) {
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	137 cat("\nT Warning : there are no individuals in common\n")
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	138 }
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	139
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	140 M2_common <- M2[M2[, 1] %in% id_common, ]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	141 #Store rows with individuals belonging only to M2
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	142 M2_specifique <- M2[! M2[, 1] %in% id_common, ]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	143 #Merge the two tables only with the samples not in common
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	144 M_merge <- bind_rows(M1, M2_specifique)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	145 col_names <- colnames(M2_common)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	146 col_names <- col_names[- which(col_names == identifiers_2)]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	147 feature_common <- check_features(M_merge, M2_bf)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	148 #Check if M_merge and M2_bf have columns in common. If so, complete the table with the values not taken.
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	149 if (!is.null(feature_common)) {
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	150
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	151 identifiers_3 <- M2_specifique[, 1]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	152 #We select the value in M2_bf, the M2 table before undergoing any changes, then insert it in the M_merge table.
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	153 for (feature in feature_common) {
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	154 for (id in identifiers_3) {
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	155
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	156 index_row <- which(M2_bf[, 1] == id)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	157 index_col <- which(colnames(M2_bf) == feature)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	158 new_value <- M2_bf[index_row, index_col]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	159 index_row <- which(M_merge[, 1] == id)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	160 index_col <- which(colnames(M_merge) == feature)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	161 M_merge[index_row, index_col] <- new_value
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	162
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	163 }
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	164 }
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	165 }
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	166 #Fill in the table with common values
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	167 for (col in col_names) {
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	168 for (id in id_common) {
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	169 index_row <- which(M2_common[, 1] == id)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	170 index_col <- which(colnames(M2_common) == col)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	171 new_value <- M2_common[index_row, index_col]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	172 index_row <- which(M_merge[, 1] == id)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	173 index_col <- which(colnames(M_merge) == col)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	174 M_merge[index_row, index_col] <- new_value
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	175
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	176 }
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	177 }
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	178 }
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	179 M_merge_sort <- M_merge[order(M_merge$order1, M_merge$order2), ]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	180 M_merge_sort <- M_merge_sort[, - which(colnames(M_merge_sort) == "order1")]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	181 M_merge_sort <- M_merge_sort[, - which(colnames(M_merge_sort) == "order2")]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	182 #DataMatrix ---------------------------------------------------------------------
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	183
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	184 colnames_1 <- colnames(DM1)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	185 colnames_2 <- colnames(DM2)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	186 #Unique -------------------------------------------------------------------------
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	187
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	188 if (concatenation == "unique") {
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	189
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	190 if (type == "sample") {
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	191
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	192 rownames(DM1) <- DM1[, 1]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	193 DM1 <- DM1[, -1]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	194 DM1 <- t(DM1)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	195 DM1 <- data.frame(sample = row.names(DM1), DM1, check.names = FALSE)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	196 colnames(DM1)[1] <- corner_DM1
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	197 rownames(DM1) <- NULL
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	198
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	199 rownames(DM2) <- DM2[, 1]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	200 DM2 <- DM2[, -1, drop = FALSE]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	201 DM2 <- t(DM2)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	202 DM2 <- data.frame(sample = row.names(DM2), DM2, check.names = FALSE)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	203 colnames(DM2)[1] <- corner_DM2
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	204 rownames(DM2) <- NULL
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	205 }
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	206 result <- list(M_merge_sort = M_merge_sort, DM1 = DM1, DM2 = DM2)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	207 return(result)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	208 }
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	209
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	210 #Intersection--------------------------------------------------------------------
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	211
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	212 if (concatenation == "intersection") {
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	213
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	214 id_in_common <- intersect(DM1[, 1], DM2[, 1])
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	215
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	216 DM1_filter <- subset(DM1, DM1[, 1] %in% id_in_common)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	217 DM2_filter <- subset(DM2, DM2[, 1] %in% id_in_common)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	218
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	219 if (type == "sample") {
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	220
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	221 rownames(DM1_filter) <- DM1_filter[, 1]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	222 DM1_filter <- DM1_filter[, -1]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	223 DM1_filter <- t(DM1_filter)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	224 DM1_filter <- data.frame(sample = row.names(DM1_filter), DM1_filter, check.names = FALSE)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	225 colnames(DM1_filter)[1] <- corner_DM1
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	226 rownames(DM1_filter) <- NULL
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	227
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	228 rownames(DM2_filter) <- DM2_filter[, 1]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	229 DM2_filter <- DM2_filter[, -1, drop = FALSE]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	230 DM2_filter <- t(DM2_filter)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	231 DM2_filter <- data.frame(sample = row.names(DM2_filter), DM2_filter, check.names = FALSE)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	232 colnames(DM2_filter)[1] <- corner_DM2
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	233 rownames(DM2_filter) <- NULL
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	234 }
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	235 result <- list(M_merge_sort = M_merge_sort, DM1 = DM1_filter, DM2 = DM2_filter)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	236 return(result)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	237 }
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	238
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	239 #Union --------------------------------------------------------------------------
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	240
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	241 if (concatenation == "union") {
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	242
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	243 common_individuals <- intersect(DM1[, 1], DM2[, 1])
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	244 common_columns <- intersect(colnames_1, colnames_2)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	245 #check whether there are individuals or variables in common
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	246 if (is.null(common_individuals) \|\| is.null(common_columns)) {
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	247
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	248 comparison_result <- FALSE
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	249 #If the individuals in common take the same values for all variables, then comparison_result=TRUE
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	250 } else {
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	251
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	252 DM1_common <- subset(DM1, DM1[, 1] %in% common_individuals)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	253 DM2_common <- subset(DM2, DM2[, 1] %in% common_individuals)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	254 DM1_common <- DM1_common[, common_columns, drop = FALSE]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	255 DM2_common <- DM2_common[, common_columns, drop = FALSE]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	256
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	257 for (col in common_columns) {
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	258 comparison_result <- identical(DM1_common$col, DM2_common$col)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	259 }
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	260
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	261 }
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	262
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	263 if (comparison_result) {
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	264
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	265
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	266 DM1$order1 <- seq(1, nrow(DM1))
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	267 DM2$order2 <- seq(nrow(DM1) + 1, nrow(DM2) + nrow(DM1))
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	268 DM1_sort <- DM1[order(DM1[, 1]), ]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	269 DM2_sort <- DM2[order(DM2[, 1]), ]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	270 id_in_common <- intersect(DM1[, 1], DM2[, 1])
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	271 DM1_filter <- subset(DM1, DM1[, 1] %in% id_in_common)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	272 DM2_filter <- subset(DM2, DM2[, 1] %in% id_in_common)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	273 different_DM2 <- colnames_2[! colnames_2 %in% colnames_1]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	274 DM2_specifique <- DM2[! DM2[, 1] %in% id_in_common, ]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	275 #Merge the two tables only with the samples not in common
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	276 DM1_merge <- bind_rows(DM1, DM2_specifique)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	277
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	278
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	279 #Deletion of columns present only in DM2
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	280 DM1_merge <- DM1_merge[, ! names(DM1_merge) %in% different_DM2]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	281 different_DM1 <- colnames_1[! colnames_1 %in% colnames_2]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	282 DM1_specifique <- DM1[! DM1[, 1] %in% id_in_common, ]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	283 #Merge the two tables only with the samples not in common
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	284 DM2_merge <- bind_rows(DM2, DM1_specifique)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	285 #Deletion of columns present only in DM2
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	286 DM2_merge <- DM2_merge[, ! names(DM2_merge) %in% different_DM1]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	287 #DM2_merge
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	288
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	289
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	290 DM1_merge_sort <- DM1_merge[order(DM1_merge$order1, DM1_merge$order2), ]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	291 DM1_merge_sort <- DM1_merge_sort[, - which(colnames(DM1_merge_sort) == "order1")]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	292 DM1_merge_sort <- DM1_merge_sort[, - which(colnames(DM1_merge_sort) == "order2")]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	293
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	294 DM2_merge_sort <- DM2_merge[order(DM2_merge$order1, DM2_merge$order2), ]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	295 DM2_merge_sort <- DM2_merge_sort[, - which(colnames(DM2_merge_sort) == "order1")]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	296 DM2_merge_sort <- DM2_merge_sort[, - which(colnames(DM2_merge_sort) == "order2")]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	297
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	298
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	299 if (type == "sample") {
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	300
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	301 rownames(DM1_merge_sort) <- DM1_merge_sort[, 1]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	302 DM1_merge_sort <- DM1_merge_sort[, -1]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	303 DM1_merge_sort <- t(DM1_merge_sort)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	304 DM1_merge_sort <- data.frame(sample = row.names(DM1_merge_sort), DM1_merge_sort, check.names = FALSE)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	305 colnames(DM1_merge_sort)[1] <- corner_DM1
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	306 rownames(DM1_merge_sort) <- NULL
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	307
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	308 rownames(DM2_merge_sort) <- DM2_merge_sort[, 1]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	309 DM2_merge_sort <- DM2_merge_sort[, -1, drop = FALSE]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	310 DM2_merge_sort <- t(DM2_merge_sort)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	311 DM2_merge_sort <- data.frame(sample = row.names(DM2_merge_sort), DM2_merge_sort, check.names = FALSE)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	312 colnames(DM2_merge_sort)[1] <- corner_DM2
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	313 rownames(DM2_merge_sort) <- NULL
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	314 }
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	315
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	316 result <- list(M_merge_sort = M_merge_sort, DM1 = DM1_merge_sort, DM2 = DM2_merge_sort)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	317 return(result)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	318
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	319 } else {
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	320 #selects line ids that are in DM2 and not in DM1
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	321 id_diff_1 <- setdiff(DM2[, 1], DM1[, 1])
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	322 #we store them in a dataframe
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	323 row_add_1 <- data.frame(id = id_diff_1)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	324 #renames columns with their names in DM1
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	325 colnames(row_add_1)[1] <- colnames(DM1)[1]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	326 #Merge
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	327 DM1_add <- bind_rows(DM1, row_add_1)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	328 id_diff_2 <- setdiff(DM1[, 1], DM2[, 1])
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	329 row_add_2 <- data.frame(id = id_diff_2)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	330 colnames(row_add_2)[1] <- colnames(DM2)[1]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	331 DM2_add <- bind_rows(DM2, row_add_2)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	332
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	333 if (type == "sample") {
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	334 rownames(DM1_add) <- DM1_add[, 1]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	335 DM1_add <- DM1_add[, -1]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	336 DM1_add <- t(DM1_add)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	337 DM1_add <- data.frame(sample = row.names(DM1_add), DM1_add, check.names = FALSE)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	338 colnames(DM1_add)[1] <- corner_DM1
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	339 rownames(DM1_add) <- NULL
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	340 rownames(DM2_add) <- DM2_add[, 1]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	341 DM2_add <- DM2_add[, -1, drop = FALSE]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	342 DM2_add <- t(DM2_add)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	343 DM2_add <- data.frame(sample = row.names(DM2_add), DM2_add, check.names = FALSE)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	344 colnames(DM2_add)[1] <- corner_DM2
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	345 rownames(DM2_add) <- NULL
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	346 }
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	347 result <- list(M_merge_sort = M_merge_sort, DM1 = DM1_add, DM2 = DM2_add)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	348 return(result)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	349
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	350 }
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	351 }
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec workflow4metabolomics parents: diff changeset	352 }

Mercurial > repos > workflow4metabolomics > w4mconcatenate

annotate concatenation.R @ 0:c577f13705f2 draft default tip