Changed prop.T in oneStepSim

DESCRIPTION

@@ -1,13 +1,13 @@
 Package: simDeNet
 Type: Package
-Title: Simulation study on deconvolution for network estimate
-Version: 0.0.2
-Date: 2017-02-03
-Author: Yun Zhang
+Title: Simulation study on deconvolution for co-expression network
+Version: 1.0.0
+Date: 2019-04-22
+Author: Yun Zhang, Jonavelle Cuerdo, Matthew McCall
 Maintainer: Yun Zhang <yun_zhang@urmc.rochester.edu>
 Description: This package is built for reproducibility of the simulation study.
-Depends: R (>= 3.3.0)
-Imports: mvtnorm, preprocessCore, ISOpureR, ROCR, WGCNA, minet, bnlearn
+Depends: R (>= 3.5.0)
+Imports: methods, mvtnorm, preprocessCore, ISOpureR, ROCR, shiny
 VignetteBuilder: knitr
-Suggests: knitr, rmarkdown
+Suggests: knitr, rmarkdown, shinydashboard, DT, GeneNet, abind
 License: GPL-3

NAMESPACE

@@ -4,9 +4,9 @@ importFrom(ISOpureR, ISOpure.step1.CPE, ISOpure.step2.PPE)
 importFrom(ROCR, prediction, performance, plot)
 importClassesFrom(ROCR, performance, prediction)
 importMethodsFrom(ROCR, plot)
-importFrom(WGCNA, adjacency)
-importFrom(minet, minet)
-importFrom(bnlearn, hc, bn.fit)
+importFrom("graphics", "legend")
+importFrom("methods", "slot", "slot<-")
+importFrom("stats", "runif")
+importFrom("shiny", "runApp")
 
-
-export(oneStepSim, generate.Sigma, sim.expr, deconv, eval.ROC, netEstByMethod)
+export(oneStepSim, generate.Sigma, sim.expr, deconv, eval.ROC, runShiny)

R/eval.ROC.R

@@ -5,7 +5,7 @@
 ##############
 
 
-eval.ROC <- function(est.str, true.str, plot.ROC=TRUE, show.AUC=TRUE, zoom=TRUE, ...){
+eval.ROC <- function(est.str, true.str, plot.ROC=TRUE, show.AUC=TRUE, zoom=FALSE, lightPDF=FALSE, ...){
   # if(sum(dim(est.str)!=dim(est.str))>0){stop("Error: est.str and true.str must have the same dimemsion.")}
   # if(!isSymmetric(unname(est.str))|!isSymmetric(unname(true.str))){stop("Error: est.str and true.str must be symmetric.")}
 
@@ -23,8 +23,15 @@ eval.ROC <- function(est.str, true.str, plot.ROC=TRUE, show.AUC=TRUE, zoom=TRUE,
 
   ## plot
   if(plot.ROC){
-    if(zoom){plot(perf, xlim=c(0,xval), ylim=c(0,yval), ...)}
-    else plot(perf)
+    perf.plot <- perf
+    if(lightPDF){
+      set.seed = 123
+      sparsePoints <- c(1, sort(sample(2:(n.unique-1), 10000)), n.unique)
+      slot(perf.plot,"x.values")[[1]] <- slot(perf.plot,"x.values")[[1]][sparsePoints]
+      slot(perf.plot,"y.values")[[1]] <- slot(perf.plot,"y.values")[[1]][sparsePoints]
+    }
+    if(zoom){plot(perf.plot, xlim=c(0,xval), ylim=c(0,yval), ...)}
+    else plot(perf.plot, ...)
     if(show.AUC){legend("bottom",paste0("AUC=",round(auc.value,3)),bty = "n")}
   }
 

R/oneStepSim.R

@@ -34,7 +34,7 @@ oneStepSim <- function(n.samp, mu.T, mu.N, Sigma.T=NULL, Sigma.N=NULL, prop.T="s
 
   return(list("m.gene"=m.gene, "Sigma.T"=Sigma.T, "Sigma.N"=Sigma.N, "true.str.T"=true.str.T,
               "expr.pure.T"=out.expr$expr.pure.T, "expr.pure.N"=out.expr$expr.pure.N, 
-              "expr.mixed"=out.expr$expr.mixed, "true.prop"=prop.T))
+              "expr.mixed"=out.expr$expr.mixed, "true.prop"=out.expr$true.prop))
 }
 
 
@@ -95,6 +95,7 @@ generate.Sigma <- function(m.gene, block.size, rho, dd=NULL, str.type="interchan
   if(sum(block.size)>m.gene){stop("Error: sum of block.size must be smaller than m.gene.")}
   if(length(rho)!=length(block.size)){stop("Error: rho and block.size must be have the same length.")}
   if(!is.null(dd)&length(dd)!=m.gene){stop("Error: dd must have length equal to m.gene.")}
+  if(length(str.type)!=length(block.size)&length(str.type)!=1){stop("Error: either specify one str.type for all the blocks or specify different str.type for each block.")}
 
   ## weight matrix
   if(is.null(dd)){dd <- rep(1,m.gene)}

R/runShiny.R

@@ -0,0 +1,8 @@
+runShiny <- function() {
+  appDir <- system.file("shinyapp", package = "simDeNet")
+  if (appDir == "") {
+    stop("Could not find example directory. Try re-installing `simDeNet`.", call. = FALSE)
+  }
+
+  shiny::runApp(appDir, display.mode = "normal")
+}

README.md

@@ -1 +1,25 @@
-# simDeNet-R-Package
+# Interactive exploration of the effect of tissue composition on gene co-expression
+
+## Getting Started
+
+Install package:
+```R
+install.packages("devtools")
+devtools::install_github("yunzhang813/simDeNet-R-Package-Shiny")
+```
+
+Launch Shiny application for interactive exploration using pre-uploaded pure cell type data:
+```R
+library(simDeNet)
+runShiny()
+```
+![](vignettes/Shiny-steps.png)
+
+
+Browse vignette for other useful functions included in the pakcage:
+```R
+browseVignettes("simDeNet")
+```
+
+## Citation
+Yun Zhang, Jonavelle Cuerdo, Marc K Halushka, Matthew N McCall, 2019. The effect of tissue composition on gene co-expression, *Briefings in Bioinformatics*, bbz135, https://doi.org/10.1093/bib/bbz135

data/datalist

@@ -1 +1 @@
-celltype
+celltype