New vignette - meta ms peaks!

xia-lab · Nov 18, 2020 · 57e0abe · 57e0abe
1 parent f603a56
commit 57e0abe
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Showing 27 changed files with 14,356 additions and 151 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -68,6 +68,8 @@ Suggests:
     devtools,
     testthat,
     plotly,
+    visnetwork,
+    ggraph,
     reshape2,
     RSclient,
     MSnbase,

diff --git a/NAMESPACE b/NAMESPACE
@@ -262,6 +262,7 @@ export(PlotKmeans)
 export(PlotLoadingCmpd)
 export(PlotMBTimeProfile)
 export(PlotMSEA.Overview)
+export(PlotMSPeaksCpdEcpdNetwork)
 export(PlotMSPeaksPerm)
 export(PlotMetaVenn)
 export(PlotMetpaPath)
@@ -292,6 +293,7 @@ export(PlotPLSLoading)
 export(PlotPLSPairSummary)
 export(PlotPathSummary)
 export(PlotPathwayMZHits)
+export(PlotPathwayMetaAnalysis)
 export(PlotPeaks2Paths)
 export(PlotPowerProfile)
 export(PlotPowerStat)

diff --git a/R/enrich_name_match.R b/R/enrich_name_match.R
@@ -17,7 +17,7 @@
 #'@export
 
 CrossReferencing <- function(mSetObj=NA, q.type, hmdb=T, pubchem=T, chebi=F, kegg=T, metlin=F){
-  
+
   mSetObj <- .get.mSet(mSetObj);
 
   # record the filter for 8 major databases

diff --git a/R/enrich_path_stats.R b/R/enrich_path_stats.R
@@ -180,14 +180,12 @@ GetORA.pathNames <- function(mSetObj=NA){
 
 # contains three inner functions to be compatible with microservice
 CalculateQeaScore <- function(mSetObj=NA, nodeImp, method){
-  
+
   mSetObj <- .get.mSet(mSetObj);
-  mSetObj <- .prepare.qea.score(mSetObj, nodeImp, method); # on local, everything is done
 
-  if(.on.public.web){
-    .perform.computing();
-    mSetObj <- .save.qea.score(mSetObj);  
-  }
+  mSetObj <- .prepare.qea.score(mSetObj, nodeImp, method); # on local, everything is done
+  .perform.computing();
+  mSetObj <- .save.qea.score(mSetObj);  
 
   return(.set.mSet(mSetObj));
 }
@@ -233,7 +231,7 @@ CalculateQeaScore <- function(mSetObj=NA, nodeImp, method){
 
   names(univ.p) <- colnames(path.data);
 
-  if(!.on.public.web & mSetObj$pathwaylibtype == "KEGG"){
+  if(!.on.public.web & mSetObj$pathwaylibtype == "KEGG" & !exists("current.kegglib")){
     mSetObj$api$nodeImp <- nodeImp;
     mSetObj$api$method <- method;
     mSetObj$api$pathDataColNms <- colnames(path.data)
@@ -296,7 +294,7 @@ CalculateQeaScore <- function(mSetObj=NA, nodeImp, method){
     mSetObj$analSet$qea.filtered.mset <- current.mset;
     uniq.count <- length(unique(unlist(current.mset), use.names=FALSE));
   }
-  
+
   hits <- lapply(current.mset, function(x) {x[x %in% colnames(path.data)]});
   hit.inx <- unlist(lapply(hits, function(x) {length(x)}), use.names=FALSE) > 0;
   hits <- hits[hit.inx]; # remove no hits

diff --git a/R/enrich_stats.R b/R/enrich_stats.R
@@ -177,7 +177,7 @@ CalculateGlobalTestScore <- function(mSetObj=NA){
   msea.data <- mSetObj$dataSet$norm[,hit.inx];
   colnames(msea.data) <- nm.map$hmdb[hmdb.inx[hit.inx]];
 
-  if(!.on.public.web & grepl("kegg", mSetObj$analSet$msetlibname)){
+  if(!.on.public.web & grepl("kegg", mSetObj$analSet$msetlibname) & !exists("current.msetlib")){
 
     mSetObj$api$mseaDataColNms <- colnames(msea.data)
     msea.data <- as.matrix(msea.data)
@@ -243,7 +243,7 @@ CalculateGlobalTestScore <- function(mSetObj=NA){
   }
 
   set.num <- unlist(lapply(current.mset, length), use.names = FALSE);
-  
+
   # first, get the matched entries from current.mset
   hits <- lapply(current.mset, function(x){x[x %in% colnames(msea.data)]});
   phenotype <- mSetObj$dataSet$cls;

diff --git a/R/general_misc_utils.R b/R/general_misc_utils.R
@@ -198,7 +198,7 @@ UnzipUploadedFile<-function(inPath, outPath, rmFile=T){
 #'
 
 CleanData <-function(bdata, removeNA=T, removeNeg=T, removeConst=T){
-  
+
   if(sum(bdata==Inf, na.rm=TRUE)>0){
     inx <- bdata == Inf;
     bdata[inx] <- NA;

diff --git a/R/general_proc_utils.R b/R/general_proc_utils.R
@@ -478,7 +478,7 @@ FilterVariable <- function(mSetObj=NA, filter, qcFilter, rsd){
       msg <- paste(msg, "Further feature filtering based on", nm);
 
       if(mSetObj$analSet$type == "mummichog"){
-        max.allow <- 10000;
+        max.allow <- 5000;
       }else if(mSetObj$analSet$type == "power"){
         max.allow <- 5000;
       }else{