Mercurial > repos > recetox > ramclustr

comparison ramclustr_wrapper.R @ 4:050cfef6ba65 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
author recetox
date Thu, 15 Jun 2023 14:01:48 +0000
parents 2ec9253a647e
children 09cabbc3d12d
comparison
equal deleted inserted replaced
3:2ec9253a647e 4:050cfef6ba65
1 store_output <- function(ramclustr_obj, 1 store_output <- function(ramclustr_obj,
2 output_merge_msp, 2 output_merge_msp,
3 output_spec_abundance, 3 output_spec_abundance,
4 msp_file) { 4 msp_file) {
5 RAMClustR::write.msp(ramclustr_obj, one.file = output_merge_msp) 5 RAMClustR::write.msp(ramclustr_obj, one.file = output_merge_msp)
6 write.csv(ramclustr_obj$SpecAbund, file = output_spec_abundance, row.names = TRUE, quote = FALSE) 6 write.csv(ramclustr_obj$SpecAbund,
7 file = output_spec_abundance,
8 row.names = TRUE, quote = FALSE
9 )
7 10
8 if (!is.null(msp_file)) { 11 if (!is.null(msp_file)) {
9 exp_name <- ramclustr_obj$ExpDes[[1]][which(row.names(ramclustr_obj$ExpDes[[1]]) == "Experiment"), 1] 12 exp_name <- ramclustr_obj$ExpDes[[1]][which(
13 row.names(ramclustr_obj$ExpDes[[1]]) == "Experiment"
14 ), 1]
10 filename <- paste("spectra/", exp_name, ".msp", sep = "") 15 filename <- paste("spectra/", exp_name, ".msp", sep = "")
11 file.copy(from = filename, to = msp_file, overwrite = TRUE) 16 file.copy(from = filename, to = msp_file, overwrite = TRUE)
12 } 17 }
13 } 18 }
14 19
33 } 38 }
34 39
35 return(data) 40 return(data)
36 } 41 }
37 42
38 ramclustr_xcms <- function(input_xcms, 43 read_ramclustr_aplcms <- function(ms1_featuredefinitions = NULL,
39 use_pheno, 44 ms1_featurevalues = NULL,
40 sr, 45 df_phenodata = NULL,
41 st = NULL, 46 phenodata_ext = NULL,
42 cor_method, 47 exp_des = NULL,
43 maxt, 48 st = NULL,
44 linkage, 49 ensure_no_na = TRUE) {
45 min_module_size, 50 ms1_featuredefinitions <- arrow::read_parquet(ms1_featuredefinitions)
46 hmax, 51 ms1_featurevalues <- arrow::read_parquet(ms1_featurevalues)
47 deep_split,
48 normalize,
49 metadata_file = NULL,
50 qc_inj_range,
51 block_size,
52 mult,
53 mzdec,
54 rt_only_low_n,
55 replace_zeros,
56 exp_design = NULL) {
57 obj <- load(input_xcms)
58 52
53 if (!is.null(df_phenodata)) {
54 if (phenodata_ext == "csv") {
55 df_phenodata <- read.csv(
56 file = df_phenodata,
57 header = TRUE, check.names = FALSE
58 )
59 } else {
60 df_phenodata <- read.csv(
61 file = df_phenodata,
62 header = TRUE, check.names = FALSE, sep = "\t"
63 )
64 }
65 }
66 if (!is.null(exp_des)) {
67 exp_des <- load_experiment_definition(exp_des)
68 }
69
70 feature_values <- ms1_featurevalues[-1]
71 feature_values <- t(feature_values)
72 colnames(feature_values) <- ms1_featurevalues[[1]]
73
74 feature_definitions <- data.frame(ms1_featuredefinitions)
75
76 ramclustr_obj <- RAMClustR::rc.get.df.data(
77 ms1_featureDefinitions = feature_definitions,
78 ms1_featureValues = feature_values,
79 phenoData = df_phenodata,
80 ExpDes = exp_des,
81 st = st,
82 ensure.no.na = ensure_no_na
83 )
84 return(ramclustr_obj)
85 }
86
87 apply_normalisation <- function(ramclustr_obj = NULL,
88 normalize_method,
89 metadata_file = NULL,
90 qc_inj_range,
91 p_cut,
92 rsq_cut,
93 p_adjust) {
59 batch <- NULL 94 batch <- NULL
60 order <- NULL 95 order <- NULL
61 qc <- NULL 96 qc <- NULL
62 97
63 if (!is.null(metadata_file)) { 98 if (normalize_method == "TIC") {
64 metadata <- read_metadata(metadata_file) 99 ramclustr_obj <- RAMClustR::rc.feature.normalize.tic(
65 batch <- metadata$batch 100 ramclustObj =
66 order <- metadata$order 101 ramclustr_obj
67 qc <- metadata$qc 102 )
103 } else if (normalize_method == "quantile") {
104 ramclustr_obj <- RAMClustR::rc.feature.normalize.quantile(ramclustr_obj)
105 } else if (normalize_method == "batch.qc") {
106 if (!(is.null(metadata_file) || metadata_file == "None")) {
107 metadata <- read_metadata(metadata_file)
108 batch <- metadata$batch
109 order <- metadata$order
110 qc <- metadata$qc
111 }
112
113 ramclustr_obj <- RAMClustR::rc.feature.normalize.batch.qc(
114 order = order,
115 batch = batch,
116 qc = qc,
117 ramclustObj = ramclustr_obj,
118 qc.inj.range = qc_inj_range
119 )
120 } else {
121 if (!(is.null(metadata_file) || metadata_file == "None")) {
122 metadata <- read_metadata(metadata_file)
123 batch <- metadata$batch
124 order <- metadata$order
125 qc <- metadata$qc
126 }
127
128 ramclustr_obj <- RAMClustR::rc.feature.normalize.qc(
129 order = order,
130 batch = batch,
131 qc = qc,
132 ramclustObj = ramclustr_obj,
133 p.cut = p_cut,
134 rsq.cut = rsq_cut,
135 p.adjust = p_adjust
136 )
68 } 137 }
69 138 return(ramclustr_obj)
70 experiment <- NULL
71
72 if (!is.null(exp_design)) {
73 experiment <- load_experiment_definition(exp_design)
74 }
75
76 x <- RAMClustR::ramclustR(
77 xcmsObj = xdata,
78 st = st,
79 maxt = maxt,
80 sr = sr,
81 deepSplit = deep_split,
82 blocksize = block_size,
83 mult = mult,
84 hmax = hmax,
85 usePheno = use_pheno,
86 mspout = FALSE,
87 qc.inj.range = qc_inj_range,
88 normalize = normalize,
89 minModuleSize = min_module_size,
90 linkage = linkage,
91 mzdec = mzdec,
92 cor.method = cor_method,
93 rt.only.low.n = rt_only_low_n,
94 fftempdir = NULL,
95 replace.zeros = replace_zeros,
96 batch = batch,
97 order = order,
98 qc = qc,
99 ExpDes = experiment
100 )
101 return(x)
102 } 139 }
103
104 ramclustr_csv <- function(ms,
105 idmsms,
106 sr,
107 st,
108 cor_method,
109 maxt,
110 linkage,
111 min_module_size,
112 hmax,
113 deep_split,
114 normalize,
115 metadata_file = NULL,
116 qc_inj_range,
117 block_size,
118 mult,
119 mzdec,
120 rt_only_low_n,
121 replace_zeros,
122 exp_design = NULL) {
123 if (!file.exists(idmsms)) {
124 idmsms <- NULL
125 }
126
127 batch <- NULL
128 order <- NULL
129 qc <- NULL
130
131 if (!is.null(metadata_file)) {
132 metadata <- read_metadata(metadata_file)
133 batch <- metadata$batch
134 order <- metadata$order
135 qc <- metadata$qc
136 }
137
138 experiment <- NULL
139
140 if (!is.null(exp_design)) {
141 experiment <- load_experiment_definition(exp_design)
142 }
143
144 x <- RAMClustR::ramclustR(
145 ms = ms,
146 idmsms = idmsms,
147 st = st,
148 maxt = maxt,
149 sr = sr,
150 deepSplit = deep_split,
151 blocksize = block_size,
152 mult = mult,
153 hmax = hmax,
154 mspout = FALSE,
155 qc.inj.range = qc_inj_range,
156 normalize = normalize,
157 minModuleSize = min_module_size,
158 linkage = linkage,
159 mzdec = mzdec,
160 cor.method = cor_method,
161 rt.only.low.n = rt_only_low_n,
162 fftempdir = NULL,
163 replace.zeros = replace_zeros,
164 batch = batch,
165 order = order,
166 qc = qc,
167 ExpDes = experiment
168 )
169 return(x)
170 }