Cobra docs (#298)

* update documentation * remove monster tests * reduce monstr test * update documentation * remove diffedge example * reduce monster tests * remove spider example * update monster examples * remove lioness tests * remove pada tests * add citation * add cobra docs * build new website * update package * update package * add package * export pandaR classes * add site html * import classes from PANDA * import classes from PANDA * import classes from PANDA * import classes from PANDA * import classes from PANDA * import classes from PANDA * import classes from PANDA
netZoo · Sep 25, 2023 · ed3439f · ed3439f
1 parent 9be1495
commit ed3439f
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diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -63,6 +63,14 @@ jobs:
             extSoftVersion()["BLAS"]
         shell: Rscript {0}
 
+      - if: matrix.os == 'ubuntu-latest'
+        run: |
+          sudo apt-get install python3-venv
+          pip install --upgrade pip
+          python3 -m venv env
+          source env/bin/activate
+          echo "VIRTUAL ENV:" $VIRTUAL_ENV
+
       - name: Install reticulate
         run: |
             library("reticulate")

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: netZooR
 Type: Package
 Title: Unified methods for the inference and analysis of gene regulatory networks
-Version: 1.4.0
-Date: 2023-06-03
+Version: 1.5.4
+Date: 2023-09-25
 Authors@R: c(person("Marouen", "Ben Guebila",
 			email = "benguebila@hsph.harvard.edu", role = c("aut","cre"), comment = c(ORCID = "0000-0001-5934-966X")),
 	     person("Tian", "Wang", 
@@ -24,11 +24,12 @@ Description: netZooR unifies the implementations of several Network Zoo methods
 Depends: R (>= 4.2.0),
    	 igraph,
 	 reticulate,
-         pandaR,
          yarn,
+	 pandaR,
          matrixcalc
 Remotes: 
-	 stan-dev/cmdstanr 
+	 stan-dev/cmdstanr,
+	 jnpaulson/pandaR 
 biocViews:
 	 NetworkInference,
 	 Network,

diff --git a/NAMESPACE b/NAMESPACE
@@ -1,11 +1,11 @@
 # Generated by roxygen2: do not edit by hand
 
-export(TIGER)
 export(adj2el)
 export(adj2regulon)
 export(alpaca)
 export(alpacaCrane)
 export(alpacaExtractTopGenes)
+export(cobra)
 export(condorCluster)
 export(condorCoreEnrich)
 export(condorMatrixModularity)
@@ -41,12 +41,13 @@ export(pandaDiffEdges)
 export(pandaPy)
 export(pandaToAlpaca)
 export(pandaToCondorObject)
-export(prior.pp)
+export(priorPp)
 export(puma)
 export(runEgret)
 export(sambar)
 export(sourcePPI)
 export(spider)
+export(tiger)
 export(visPandaInCytoscape)
 import(AnnotationDbi, except= select)
 

diff --git a/R/COBRA.R b/R/COBRA.R
@@ -45,7 +45,7 @@ cobra <- function(X, expressionData, standardize=T){
     G <- as.matrix(G)
   }
 
-  eigenG <- eigs_sym(tcrossprod(G),N)
+  eigenG <- rARPACK::eigs_sym(tcrossprod(G),N)
 
   Q <- eigenG$vectors
   D <- diag(eigenG$values)

diff --git a/R/PANDA.R b/R/PANDA.R
@@ -201,4 +201,3 @@ pandaPy <- function(expr_file, motif_file=NULL, ppi_file=NULL, computing="cpu",
   return(output)
 }  
 
-
diff --git a/R/PUMA.R b/R/PUMA.R
@@ -422,5 +422,3 @@ prepResult <- function(zScale, output, regulatoryNetwork, geneCoreg, tfCoopNetwo
   pandaObj(regNet=regulatoryNetwork, coregNet=geneCoreg, coopNet=tfCoopNetwork, numGenes=numGenes, numTFs=numTFs, numEdges=numEdges)
 }
 
-pandaObj <- setClass("panda", slots=c("regNet","coregNet","coopNet","numGenes","numTFs","numEdges"))
-setMethod("show","panda",function(object){print.panda(object)})
diff --git a/R/SPIDER.R b/R/SPIDER.R
@@ -423,7 +423,4 @@ prepResult <- function(zScale, output, regulatoryNetwork, geneCoreg, tfCoopNetwo
     resList$coopNet <- tfCoopNetwork
   }
   pandaObj(regNet=regulatoryNetwork, coregNet=geneCoreg, coopNet=tfCoopNetwork, numGenes=numGenes, numTFs=numTFs, numEdges=numEdges)
-}
-
-pandaObj <- setClass("panda", slots=c("regNet","coregNet","coopNet","numGenes","numTFs","numEdges"))
-setMethod("show","panda",function(object){print.panda(object)})
+}
diff --git a/R/TIGER.R b/R/TIGER.R
@@ -55,8 +55,8 @@
 #' @examples
 #' data(TIGER_expr)
 #' data(TIGER_prior)
-#' TIGER(TIGER_expr,TIGER_prior)
-TIGER = function(expr,prior,method="VB",TFexpressed = TRUE,
+#' tiger(TIGER_expr,TIGER_prior)
+tiger = function(expr,prior,method="VB",TFexpressed = TRUE,
                  signed=TRUE,baseline=TRUE,psis_loo = FALSE,
                  seed=123,out_path=NULL,out_size = 300,
                  a_sigma=1,b_sigma=1,a_alpha=1,b_alpha=1,
@@ -75,7 +75,7 @@ TIGER = function(expr,prior,method="VB",TFexpressed = TRUE,
 
   #0. prepare stan input
   if (signed){
-    prior2 = prior.pp(prior[TF.name,TG.name],expr)
+    prior2 = priorPp(prior[TF.name,TG.name],expr)
     if (nrow(prior2)!=length(TF.name)){
       TFnotExp = setdiff(TF.name,rownames(prior2))
       TFnotExpEdge = prior[TFnotExp,colnames(prior2),drop=F]
@@ -292,7 +292,7 @@ adj2regulon = function(adj){
 #' @return A filtered prior network (adjacency matrix).
 #' @export
 #'
-prior.pp = function(prior,expr){
+priorPp = function(prior,expr){
 
   # filter tfs and tgs
   tf = intersect(rownames(prior),rownames(expr)) ## TF needs to express

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -1,61 +1,140 @@
+template:
+  bootstrap: 5
 destination: docs
 reference:
 - title: Main functions
   desc:  main functions to run each algorithm
   contents:
-  - panda.py
-  - create.condor.object
-  - panda.to.condor.object
-  - lioness.py
+  - pandaPy
+  - createCondorObject
   - lioness
   - alpaca
-  - panda.to.alpaca
   - sambar
   - monster
   - otter
-- title: Plot functions
-  desc: function to plot the networks and community structures.
+  - cobra
+  - puma
+  - spider
+  - tiger
+  - runEgret
+  - dragon
+  - craneBipartite
+
+- title: PANDA
+  desc: All functions of PANDA
   contents:
-  - create.panda.style
-  - create.diff.panda.style
-  - condor.plot.communities
-  - condor.plot.heatmap
-  - starts_with("vis.")
-- title: PANDA 
-  desc: All function of PANDA
-  contents:
-  - panda.py
-  - panda.to.condor.object
-  - panda.to.alpaca
-  - panda.diff.edges
-  - create.panda.style
-  - vis.panda.in.cytoscape
-  - create.panda.style
-  - vis.diff.panda.in.cytoscape
-  - create.diff.panda.style
+  - pandaPy
+  - pandaToCondorObject
+  - pandaToAlpaca
+  - pandaDiffEdges
+  - visPandaInCytoscape
+  - createPandaStyle
+
 - title: CONDOR
-  desc: All fucntions of CONDOR
-  contents: 
+  desc: All functions of CONDOR
+  contents:
+  - createCondorObject
   - starts_with("condor")
-  - create.condor.object
-- title: LIONESS 
+
+
+- title: LIONESS
   desc: All functions of LIONESS
-  contents: 
-  - lioness.py
+  contents:
+  - lionessPy
   - lioness
+
 - title: ALPACA
   desc: All functions of ALPACA
   contents:
   - starts_with("alpaca")
-- title: SAMBAR 
+
+- title: SAMBAR
   desc: All functions of SAMBAR
   contents:
   - starts_with("sambar")
+
 - title: MONSTER
   desc: All functions of MONSTER
   contents:
   - starts_with("monster")
+
 - title: OTTER
-  desc: All functions of OTTER
+  desc: OTTER functions
+  contents:
+  - otter
+
+- title : TIGER
+  desc: TIGER functions
+  contents:
+  - tiger
+  - TIGER_expr
+  - TIGER_prior
+  - adj2regulon
+  - priorPp
+
+- title : COBRA
+  desc: COBRA functions
+  contents:
+  - cobra
+
+- title: CRANE
+  desc: CRANE functions
+  contents:
+  - craneBipartite
+  - craneUnipartite
+  - elistToAdjMat
+  - elistSort
+  - elistRemoveTags
+  - elistSort
+  - isElist
+  - adjMatToElist
+  - el2adj
+  - el2regulon
+  - elistIsEdgeOrderEqual
+  - elistAddTags
+  - adj2el
+  - jutterDegree
+
+- title: DRAGON
+  desc: DRAGON functions
+  contents:
+  - dragon
+
+- title: SPIDER
+  desc: SPIDER functions
+  contents:
+  - spider
+  - degreeAdjust
+
+- title: PUMA
+  desc: PUMA functions
+  contents:
+  - puma
+
+- title: EGRET
+  desc: EGRET functions
+  contents:
+  - runEgret
+
+- title: Plotting functions
+  desc: function to plot the networks and community structures.
+  contents:
+  - createPandaStyle
+  - condorPlotCommunities
+  - condorPlotHeatmap
+
+- title: Helper functions
+  desc: miscellaneous function
+  contents:
+  - sourcePPI
+  - pandaToCondorObject
+  - pandaToAlpaca
+
+- title: Data
+  desc: Input example data files
   contents:
-  - starts_with("otter")
+  - yeast
+  - small1976
+  - mut.ucec
+  - exon.size
+  - genes