| Previous changeset 1:29ec7e3afdd4 (2019-08-01) |
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Commit message:
Uploaded |
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modified:
CorrTable/Corr_Script_samples_row.R CorrTable/Corr_wrap.r CorrTable/README.md CorrTable/test-data/output1_CorrTable.tabular CorrTable/test-data/output2_CorrTable.tabular |
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| diff -r 29ec7e3afdd4 -r 2173ad5e7750 CorrTable/Corr_Script_samples_row.R --- a/CorrTable/Corr_Script_samples_row.R Thu Aug 01 11:30:58 2019 -0400 +++ b/CorrTable/Corr_Script_samples_row.R Wed Oct 16 03:12:55 2019 -0400 |
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| @@ -254,23 +254,23 @@ if (test.corr == "yes"){ - pvalue <- vector() - for (i in 1:dim(tab.corr)[1]){ - for (j in 1:dim(tab.corr)[2]){ - suppressWarnings(corrtest <- cor.test(tab2[,i], tab1[,j], method = corr.method)) - pvalue <- c(pvalue, corrtest$p.value) - if (multi.name == "none"){ - if (corrtest$p.value > alpha){ - tab.corr[i,j] <- 0 - } - } - } - } - + repcorrtest1 <- function(vari1,vari2,corrmeth){ + suppressWarnings(corrtest <- cor.test(vari2, vari1, method = corrmeth)) + return(corrtest$p.value) + } + repcorrtest2 <- function(stab,ftab,cormeth){ + listp <- apply(X=ftab,2,repcorrtest1,vari2=stab,corrmeth=cormeth) + return(listp) + } + pvalue <- apply(X=tab1,2,repcorrtest2,ftab=tab2,cormeth=corr.method) + + if(multi.name != "none"){ - adjust <- matrix(p.adjust(pvalue, method = multi.name), nrow = dim(tab.corr)[1], ncol = dim(tab.corr)[2], byrow = T) - tab.corr[adjust > alpha] <- 0 - } + pvalue <- matrix(p.adjust(pvalue, method = multi.name), nrow = dim(tab.corr)[1], ncol = dim(tab.corr)[2]) + } + + tab.corr[pvalue > alpha] <- 0 + } @@ -416,17 +416,14 @@ } # Assign an interval to each correlation coefficient - for (i in 1:dim(melted.tab.corr)[1]){ for (j in 1:(length(cl))){ if (vect[j] == -1){ - melted$classe[i][melted$value[i] >= vect[j] - && melted$value[i] <= vect[j+1]] <- cl[j] + melted$classe[melted$value >= vect[j] & melted$value <= vect[j+1]] <- cl[j] } else { - melted$classe[i][melted$value[i] > vect[j] - && melted$value[i] <= vect[j+1]] <- cl[j] + melted$classe[melted$value > vect[j] & melted$value <= vect[j+1]] <- cl[j] } } - } + # Find the 0 and assign it the white as name if (length(which(vect == 0)) == 1) { @@ -493,5 +490,5 @@ # Function call # correlation.tab(tab1.name, tab2.name, param1.samples, param2.samples, corr.method, test.corr, alpha, multi.name, filter, - # filters.choice, threshold, reorder.var, color.heatmap, type.classes, + # filters.choice, threshold, reorder.var, plot.choice, color.heatmap, type.classes, # reg.value, irreg.vect, output1, output2) |
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| diff -r 29ec7e3afdd4 -r 2173ad5e7750 CorrTable/Corr_wrap.r --- a/CorrTable/Corr_wrap.r Thu Aug 01 11:30:58 2019 -0400 +++ b/CorrTable/Corr_wrap.r Wed Oct 16 03:12:55 2019 -0400 |
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| @@ -33,7 +33,8 @@ if(length(args) < 10){ stop("NOT enough argument !!!") } -cat('\n--------------------------------------------------------------------', +cat('\nJob starting time:\n',format(Sys.time(), "%a %d %b %Y %X"), +'\n\n--------------------------------------------------------------------', '\nParameters used in "Between-table Correlation":\n\n') print(args) cat('--------------------------------------------------------------------\n\n') @@ -76,7 +77,8 @@ cat('\n--------------------------------------------------------------------', '\nInformation about R (version, Operating System, attached or loaded packages):\n\n') sessionInfo() -cat('--------------------------------------------------------------------\n\n') +cat('--------------------------------------------------------------------\n', +'\nJob ending time:\n',format(Sys.time(), "%a %d %b %Y %X")) #delete the parameters to avoid the passage to the next tool in .RData image |
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| diff -r 29ec7e3afdd4 -r 2173ad5e7750 CorrTable/README.md --- a/CorrTable/README.md Thu Aug 01 11:30:58 2019 -0400 +++ b/CorrTable/README.md Wed Oct 16 03:12:55 2019 -0400 |
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| @@ -43,3 +43,9 @@ ----------- * Help and support: support@workflow4metabolomics.org + + +License +----------- + + * Cea Cnrs Inria Logiciel Libre License, version 2.1 (CECILL-2.1) |
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| diff -r 29ec7e3afdd4 -r 2173ad5e7750 CorrTable/test-data/output1_CorrTable.tabular --- a/CorrTable/test-data/output1_CorrTable.tabular Thu Aug 01 11:30:58 2019 -0400 +++ b/CorrTable/test-data/output1_CorrTable.tabular Wed Oct 16 03:12:55 2019 -0400 |
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| @@ -1,6 +1,6 @@ -name M200T2618 M108T2759 M253T1601 M562T393 M140T2817 M317T2417 M498T712 M897T2828 M879T105 M413T2867 M782T2391 M835T963 M324T1666 M79T1303 M567T390 M207T2257 M232T997 M997T2834 M295T842 M958T481 M150T423 M964T1077 M510T148 M454T809 -Meta01 -0.0381099621034071 -0.0308771792251864 0.335303270663461 0.340984721652527 -0.392239536011236 0.308531863601226 -0.38276470907866 0.192781243616334 0.316953616678778 0.153455904743321 -0.145045084107932 -0.364896936594001 0.320967727079532 -0.377104415194285 0.373071418741227 0.352800416562518 0.319463412900551 0.324078173113261 0.306620047017588 0.326582168629611 0.0172092079575711 0.304807387613331 0.316450509570112 0.376440463645976 -Meta09 -0.0767546658101883 -0.129626792377785 0.101928911670895 0.115483290871375 -0.0234245956756988 0.0904474725214124 -0.024461194882052 -0.121320087678368 0.130125017347287 0.308155645217747 0.0831122451923826 0.0506561387912013 0.117292511090864 -0.0123538963682085 0.0267655184532761 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-0.0866948285493421 -0.0495558714805468 0.203647127547309 -0.0528204949117596 -0.071940864021075 0.0345675482658712 -Meta23 0.326485225265319 0.304169001191892 0.00115369881122672 0.0301042258910735 -0.103162606015147 0.0537101596905055 -0.0783558303219841 0.0274704272882075 0.114237409683009 -0.0967931551436498 0.0975083134993656 -0.102156817498172 0.00470481879378514 -0.116990014334093 -0.0211850133509491 -0.0299843961961325 -0.103705033450308 0.0145444087397323 0.0736370908927353 -0.0767582436873565 0.32405558752902 0.0067286262747507 -0.0126106752475632 -0.0716433234564737 +name M200T2618 M108T2759 M253T1601 M562T393 M140T2817 M317T2417 M498T712 M897T2828 M879T105 M413T2867 M782T2391 M835T963 M324T1666 M79T1303 M567T390 M207T2257 M232T997 M997T2834 M295T842 M958T481 M150T423 M964T1077 M510T148 M454T809 +Meta01 -0.0381099621034071 -0.0308771792251864 0.335303270663461 0.340984721652527 -0.392239536011236 0.308531863601226 -0.38276470907866 0.192781243616334 0.316953616678778 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-0.0277111328940591 -0.171696474385562 -0.158841609776784 -0.0384562204512248 -0.0881771505485084 -0.0210940775418372 -0.060166862529553 -0.00276367086310437 -0.0471787341544353 -0.0764277784424161 -0.0977299103436893 +Meta22 0.120785153157455 0.0749336584503277 -0.0270536732280649 -0.0536052973820058 -0.150016784385942 -0.0632347476656861 -0.132863877612795 0.303035673758439 -0.133995542749929 0.000998502460650215 -0.139343133878119 -0.116656852987757 -0.0993268136599691 -0.128198216041191 -0.0553520708094436 0.0371066253540359 -0.0465298462059366 -0.05907858722759 -0.0866948285493421 -0.0495558714805468 0.203647127547309 -0.0528204949117596 -0.071940864021075 0.0345675482658712 +Meta23 0.326485225265319 0.304169001191892 0.00115369881122672 0.0301042258910735 -0.103162606015147 0.0537101596905055 -0.0783558303219841 0.0274704272882075 0.114237409683009 -0.0967931551436498 0.0975083134993656 -0.102156817498172 0.00470481879378514 -0.116990014334093 -0.0211850133509491 -0.0299843961961325 -0.103705033450308 0.0145444087397323 0.0736370908927353 -0.0767582436873565 0.32405558752902 0.0067286262747507 -0.0126106752475632 -0.0716433234564737 |
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| diff -r 29ec7e3afdd4 -r 2173ad5e7750 CorrTable/test-data/output2_CorrTable.tabular --- a/CorrTable/test-data/output2_CorrTable.tabular Thu Aug 01 11:30:58 2019 -0400 +++ b/CorrTable/test-data/output2_CorrTable.tabular Wed Oct 16 03:12:55 2019 -0400 |
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|