diff --git a/publication_rmd/simulation_example_fig1/figure1.Rmd b/publication_rmd/simulation_example_fig1/figure1.Rmd
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+++ b/publication_rmd/simulation_example_fig1/figure1.Rmd
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+---
+title: "figure_1"
+output:
+  html_document:
+    code_folding: hide
+---
+
+This is a simulation example that shows that confounders and batch effects impact reconstruction of gene co-expression networks. Using this example we also show that true underlying network structure can be reconstructed after principal component correction of gene expression data as described in the paper.
+
+This script generates Figure 1 in the paper -- "Addressing confounding artifacts in reconstruction of gene co-expression networks"
+
+```{r}
+rm(list = ls())
+
+## load libraries
+#library(pcalg)
+library(mvtnorm)
+library(clusterGeneration)
+library(sva)
+#library(spacejam)
+library(gridExtra)
+library(gtable)
+library(glasso)
+library(huge)
+library(devtools)
+install_github('alyssafrazee/RSkittleBrewer')
+library(RSkittleBrewer)
+tropical = RSkittleBrewer('tropical')
+library(ggplot2)
+library(reshape2)
+library(cowplot)
+### Data: 5 features, 10 samples
+p=8
+n=10
+
+V=diag(1,nrow=p,ncol=p)
+V[1,3]=V[3,1]=.35
+V[4,7]=V[7,4]=.3
+V[1,8]=V[8,1]=.3
+V.inv=solve(V)
+
+colnames(V)=rownames(V)=colnames(V.inv)=rownames(V.inv)=paste(1:8)
+
+A.generating=V
+for(i in 1:p){
+  for(j in 1:p){
+    if(abs(V[i,j])>0.05){
+      A.generating[i,j]=1
+    }
+    if(abs(V[i,j])<=0.05){
+      A.generating[i,j]=0
+    }
+  }
+}
+g.generating=graph.adjacency(A.generating,mode="undirected", diag=FALSE,add.colnames=TRUE)
+
+set.seed(4747)
+data=rmvnorm((1000*n),mean=rep(1,p),sigma=V)
+rownames(data)=1:(1000*n)
+colnames(data)=1:8
+
+cor.data=cor(data)
+
+## Graph 
+lambda=seq(1,0.01,length.out=200)
+glasso.unconfounded.lambda=huge(data,lambda,method="glasso")
+glasso.adjacency.unconfounded.lambda=glasso.unconfounded.lambda$path
+glasso.graph.unconfounded.lambda=list()
+
+for(i in 1:200){
+  glasso.graph.unconfounded.lambda[[i]]=graph.adjacency(glasso.adjacency.unconfounded.lambda[[i]],mode="undirected", diag=FALSE)
+}
+
+############ Confounding ############
+data.confounded=data
+grp=rnorm(1000*n)
+for(i in 2:6){
+  data.confounded[,i] = data.confounded[,i] + 50*grp
+}
+
+rownames(data.confounded)=1:(1000*n)
+colnames(data.confounded)=1:8
+
+cor.data.confounded=cor(data.confounded)
+colnames(cor.data.confounded)=rownames(cor.data.confounded)=1:8
+
+colnames(data.confounded)=1:8
+rownames(data.confounded)=1:10000 
+
+glasso.confounded=huge(data.confounded,lambda,method="glasso")
+
+glasso.adjacency.confounded=glasso.confounded$path
+glasso.graph.confounded=list()
+for(i in 1:200){
+  glasso.graph.confounded[[i]]=graph.adjacency(glasso.adjacency.confounded[[i]],mode="undirected", diag=FALSE)
+}
+
+############ Correct for Confounding (Residuals from PC) ############
+mod=matrix(1,nrow=dim(data.confounded)[1],ncol=1)
+colnames(mod)="Intercept"
+nsv=num.sv(t(data.confounded),mod)
+
+ss=svd(data.confounded - colMeans(data.confounded))
+grp.est=ss$u[,1]
+data.corrected=data.confounded*0
+for(i in 1:8){
+  data.corrected[,i]=lm(data.confounded[,i] ~ grp.est)$residuals
+}
+
+rownames(data.corrected)=1:(1000*n)
+colnames(data.corrected)=1:8
+
+cor.data.corrected=cor(data.corrected)
+colnames(cor.data.corrected)=rownames(cor.data.corrected)=1:8
+
+
+glasso.corrected.lambda=huge(data.corrected,method="glasso",lambda)
+glasso.graph.corrected.lambda=list()
+for(i in 1:200){
+  glasso.graph.corrected.lambda[[i]]=graph.adjacency(glasso.corrected.lambda$path[[i]],mode="undirected", diag=FALSE)
+  
+}
+
+## For a given gene, samples are standard normal
+z.data=data
+for(j in 1:8){
+  mean=mean(data[,j])
+  sd=sd(data[,j])
+  z.data[,j]=(data[,j]-mean)/sd
+}
+
+z.data.confounded=data.confounded
+for(j in 1:8){
+  mean=mean(data.confounded[,j])
+  sd=sd(data.confounded[,j])
+  z.data.confounded[,j]=(data.confounded[,j]-mean)/sd
+}
+
+z.data.corrected=data.corrected
+for(j in 1:8){
+  mean=mean(data.corrected[,j])
+  sd=sd(data.corrected[,j])
+  z.data.corrected[,j]=(data.corrected[,j]-mean)/sd
+}
+
+```
+
+This part generates plots for each figure panel and saves it in a pdf
+
+```{r, echo=FALSE}
+### Plots
+
+col.expr=colorRampPalette(c("#d8b365", "#f5f5f5", "#5ab4ac"))
+col.corr=colorRampPalette(c("#ef8a62", "#f7f7f7", "#67a9cf"))
+
+at=seq(-1,1,length.out=50)
+layout=layout.circle(g.generating)
+
+## unconfounded data
+
+plot.z.data = melt(z.data[1:10,])
+plot.z.data$Var1 <- factor(plot.z.data$Var1)
+plot.z.data$Var2 <- factor(plot.z.data$Var2)
+
+plot.cor.data = melt(cor.data)
+plot.cor.data$Var1 <- factor(plot.cor.data$Var1)
+plot.cor.data$Var2 <- factor(plot.cor.data$Var2)
+
+### Panel a
+panela <- ggplot(plot.z.data, aes(Var1, Var2))+
+  geom_tile(aes(fill = value))+ 
+  scale_fill_gradientn(colours = col.expr(50), limits = c(-2.5,2.5))+theme_bw() + xlab("Sample") + ylab("Gene")
+
+### Panel b
+panelb <- ggplot(plot.cor.data, aes(Var1, Var2))+
+  geom_tile(aes(fill = value))+ 
+  scale_fill_gradientn(colours = col.corr(50), 
+                       limits = c(-1,1))+theme_bw() + xlab("Gene") + ylab("Gene")
+
+### Panel c
+pdf("panelc.pdf", height = 3, width = 3)
+plot(glasso.graph.unconfounded.lambda[[150]],layout=layout,vertex.label=1:8,vertex.size=50,edge.color="limegreen",edge.width=4, vertex.color="cornsilk")
+dev.off()
+
+
+## confounded
+plot.z.data.confounded = melt(z.data.confounded[1:10,])
+plot.z.data.confounded$Var1 <- factor(plot.z.data.confounded$Var1)
+plot.z.data.confounded$Var2 <- factor(plot.z.data.confounded$Var2)
+
+plot.cor.data.confounded = melt(cor.data.confounded)
+plot.cor.data.confounded$Var1 <- factor(plot.cor.data.confounded$Var1)
+plot.cor.data.confounded$Var2 <- factor(plot.cor.data.confounded$Var2)
+
+### Panel d
+paneld <- ggplot(plot.z.data.confounded, aes(Var1, Var2))+
+  geom_tile(aes(fill = value))+ 
+  scale_fill_gradientn(colours = col.expr(50), limits = c(-2.5,2.5))+theme_bw() + xlab("Sample") + ylab("Gene")
+
+
+### Panel e
+panele <- ggplot(plot.cor.data.confounded, aes(Var1, Var2))+
+  geom_tile(aes(fill = value))+ 
+  scale_fill_gradientn(colours = col.corr(50), 
+                       limits = c(-1,1))+theme_bw() + xlab("Gene") + ylab("Gene")
+
+### Panel f
+pdf("panelf.pdf", height = 3, width = 3)
+plot(glasso.graph.confounded[[150]],layout=layout,vertex.label=1:8,vertex.size=50,edge.color="limegreen",edge.width=4, vertex.color="cornsilk")
+dev.off()
+
+## corrected
+plot.z.data.corrected = melt(z.data.corrected[1:10,])
+plot.z.data.corrected$Var1 <- factor(plot.z.data.corrected$Var1)
+plot.z.data.corrected$Var2 <- factor(plot.z.data.corrected$Var2)
+
+plot.cor.data.corrected = melt(cor.data.corrected)
+plot.cor.data.corrected$Var1 <- factor(plot.cor.data.corrected$Var1)
+plot.cor.data.corrected$Var2 <- factor(plot.cor.data.corrected$Var2)
+
+### Panel g
+panelg <- ggplot(plot.z.data.corrected, aes(Var1, Var2))+
+  geom_tile(aes(fill = value))+ 
+  scale_fill_gradientn(colours = col.expr(50), limits = c(-2.5,2.5))+ theme_bw() + xlab("Sample") + ylab("Gene")
+
+
+
+### Panel h
+panelh <- ggplot(plot.cor.data.corrected, aes(Var1, Var2))+
+  geom_tile(aes(fill = value))+ 
+  scale_fill_gradientn(colours = col.corr(50), 
+                       limits = c(-1,1))+theme_bw() + xlab("Gene") + ylab("Gene")
+
+### Panel i
+pdf("paneli.pdf", height = 3, width = 3)
+plot(glasso.graph.corrected.lambda[[150]],layout=layout,vertex.label=1:8,vertex.size=50,edge.color="limegreen",edge.width=4, vertex.color="cornsilk")
+dev.off()
+
+fig1 <- plot_grid(panela + theme(legend.position="none"), 
+                  panelb + theme(legend.position="none"), 
+                  NULL, 
+                  paneld + theme(legend.position="none"), 
+                  panele + theme(legend.position="none"), 
+                  NULL, 
+                  panelg + theme(legend.position="none"), 
+                  panelh + theme(legend.position="none"), 
+                  NULL, 
+                  labels=letters[1:9], ncol = 3)
+
+legenda <- get_legend(panela + theme(legend.direction = "horizontal", legend.position = "top"))
+legendb <- get_legend(panelb + theme(legend.direction = "horizontal", legend.position = "top"))
+legend <- plot_grid(legenda, legendb, NULL, ncol = 3)
+fig1 <- plot_grid( legend, fig1, rel_heights = c(.1, 1), ncol = 1)
+
+pdf("merged.pdf", height = 6, width = 6)
+print(fig1)
+dev.off()
+```
diff --git a/publication_rmd/simulation_example_fig1/figure1.html b/publication_rmd/simulation_example_fig1/figure1.html
new file mode 100644
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+++ b/publication_rmd/simulation_example_fig1/figure1.html
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+<!DOCTYPE html>
+<html>
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
+
+<title></title>
+
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+</head>
+
+<body>
+<p>This report was automatically generated with the R package <strong>knitr</strong>
+(version 1.17).</p>
+
+<pre><code class="r">---
+title: &quot;figure_1&quot;
+output:
+  html_document:
+    code_folding: hide
+---
+
+This is a simulation example that shows that confounders and batch effects impact reconstruction of gene co-expression networks. Using this example we also show that true underlying network structure can be reconstructed after principal component correction of gene expression data as described in the paper.
+
+This script generates Figure 1 in the paper -- &quot;Addressing confounding artifacts in reconstruction of gene co-expression networks&quot;
+</code></pre>
+
+<pre><code>## Error: &lt;text&gt;:8:6: unexpected symbol
+## 7: 
+## 8: This is
+##         ^
+</code></pre>
+
+<pre><code class="r">rm(list = ls())
+
+## load libraries
+#library(pcalg)
+library(mvtnorm)
+library(clusterGeneration)
+</code></pre>
+
+<pre><code>## Loading required package: MASS
+</code></pre>
+
+<pre><code class="r">library(sva)
+</code></pre>
+
+<pre><code>## Loading required package: mgcv
+</code></pre>
+
+<pre><code>## Loading required package: nlme
+</code></pre>
+
+<pre><code>## This is mgcv 1.8-22. For overview type &#39;help(&quot;mgcv-package&quot;)&#39;.
+</code></pre>
+
+<pre><code>## Loading required package: genefilter
+</code></pre>
+
+<pre><code>## Warning: replacing previous import &#39;stats::sd&#39; by &#39;BiocGenerics::sd&#39; when
+## loading &#39;S4Vectors&#39;
+</code></pre>
+
+<pre><code>## Warning: replacing previous import &#39;stats::var&#39; by &#39;BiocGenerics::var&#39; when
+## loading &#39;S4Vectors&#39;
+</code></pre>
+
+<pre><code>## Warning: replacing previous import &#39;stats::sd&#39; by &#39;BiocGenerics::sd&#39; when
+## loading &#39;IRanges&#39;
+</code></pre>
+
+<pre><code>## Warning: replacing previous import &#39;stats::var&#39; by &#39;BiocGenerics::var&#39; when
+## loading &#39;IRanges&#39;
+</code></pre>
+
+<pre><code>## 
+## Attaching package: &#39;genefilter&#39;
+</code></pre>
+
+<pre><code>## The following object is masked from &#39;package:MASS&#39;:
+## 
+##     area
+</code></pre>
+
+<pre><code class="r">#library(spacejam)
+library(gridExtra)
+library(gtable)
+library(glasso)
+library(huge)
+</code></pre>
+
+<pre><code>## Loading required package: Matrix
+</code></pre>
+
+<pre><code>## Loading required package: lattice
+</code></pre>
+
+<pre><code>## Loading required package: igraph
+</code></pre>
+
+<pre><code>## Loading required package: methods
+</code></pre>
+
+<pre><code>## 
+## Attaching package: &#39;igraph&#39;
+</code></pre>
+
+<pre><code>## The following objects are masked from &#39;package:stats&#39;:
+## 
+##     decompose, spectrum
+</code></pre>
+
+<pre><code>## The following object is masked from &#39;package:base&#39;:
+## 
+##     union
+</code></pre>
+
+<pre><code class="r">library(devtools)
+install_github(&#39;alyssafrazee/RSkittleBrewer&#39;)
+</code></pre>
+
+<pre><code>## Skipping install of &#39;RSkittleBrewer&#39; from a github remote, the SHA1 (00881122) has not changed since last install.
+##   Use `force = TRUE` to force installation
+</code></pre>
+
+<pre><code class="r">library(RSkittleBrewer)
+tropical = RSkittleBrewer(&#39;tropical&#39;)
+library(ggplot2)
+library(reshape2)
+library(cowplot)
+</code></pre>
+
+<pre><code>## 
+## Attaching package: &#39;cowplot&#39;
+</code></pre>
+
+<pre><code>## The following object is masked from &#39;package:ggplot2&#39;:
+## 
+##     ggsave
+</code></pre>
+
+<pre><code class="r">### Data: 5 features, 10 samples
+p=8
+n=10
+
+V=diag(1,nrow=p,ncol=p)
+V[1,3]=V[3,1]=.35
+V[4,7]=V[7,4]=.3
+V[1,8]=V[8,1]=.3
+V.inv=solve(V)
+
+colnames(V)=rownames(V)=colnames(V.inv)=rownames(V.inv)=paste(1:8)
+
+A.generating=V
+for(i in 1:p){
+  for(j in 1:p){
+    if(abs(V[i,j])&gt;0.05){
+      A.generating[i,j]=1
+    }
+    if(abs(V[i,j])&lt;=0.05){
+      A.generating[i,j]=0
+    }
+  }
+}
+g.generating=graph.adjacency(A.generating,mode=&quot;undirected&quot;, diag=FALSE,add.colnames=TRUE)
+
+set.seed(4747)
+data=rmvnorm((1000*n),mean=rep(1,p),sigma=V)
+rownames(data)=1:(1000*n)
+colnames(data)=1:8
+
+cor.data=cor(data)
+
+## Graph 
+lambda=seq(1,0.01,length.out=200)
+glasso.unconfounded.lambda=huge(data,lambda,method=&quot;glasso&quot;)
+</code></pre>
+
+<pre><code>## Conducting the graphical lasso (glasso) with lossless screening....in progress:0% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:0% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:1% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:1% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:2% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:2% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:3% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:3% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:4% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:4% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:5% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:5% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:6% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:6% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:6% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:7% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:7% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:8% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:8% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:9% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:9% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:10% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:10% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:11% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:12% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:12% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:13% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:13% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:14% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:14% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:15% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:15% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:16% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:16% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:17% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:17% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:18% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:18% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:18% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:19% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:19% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:20% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:20% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:21% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:21% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:22% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:23% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:23% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:24% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:24% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:25% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:25% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:26% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:26% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:27% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:27% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:28% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:28% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:29% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:29% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:30% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:30% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:31% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:31% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:31% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:32% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:32% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:33% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:34% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:34% 
+Conducting the graphical lasso (glasso)....done.                                          
+</code></pre>
+
+<pre><code class="r">glasso.adjacency.unconfounded.lambda=glasso.unconfounded.lambda$path
+glasso.graph.unconfounded.lambda=list()
+
+for(i in 1:200){
+  glasso.graph.unconfounded.lambda[[i]]=graph.adjacency(glasso.adjacency.unconfounded.lambda[[i]],mode=&quot;undirected&quot;, diag=FALSE)
+}
+
+############ Confounding ############
+data.confounded=data
+grp=rnorm(1000*n)
+for(i in 2:6){
+  data.confounded[,i] = data.confounded[,i] + 50*grp
+}
+
+rownames(data.confounded)=1:(1000*n)
+colnames(data.confounded)=1:8
+
+cor.data.confounded=cor(data.confounded)
+colnames(cor.data.confounded)=rownames(cor.data.confounded)=1:8
+
+colnames(data.confounded)=1:8
+rownames(data.confounded)=1:10000 
+
+glasso.confounded=huge(data.confounded,lambda,method=&quot;glasso&quot;)
+</code></pre>
+
+<pre><code>## Conducting the graphical lasso (glasso) with lossless screening....in progress:0% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:0% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:1% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:1% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:2% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:2% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:3% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:3% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:4% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:4% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:5% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:5% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:6% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:6% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:6% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:7% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:7% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:8% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:8% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:9% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:9% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:10% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:10% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:11% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:12% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:12% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:13% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:13% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:14% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:14% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:15% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:15% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:16% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:16% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:17% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:17% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:18% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:18% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:18% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:19% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:19% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:20% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:20% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:21% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:21% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:22% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:23% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:23% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:24% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:24% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:25% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:25% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:26% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:26% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:27% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:27% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:28% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:28% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:29% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:29% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:30% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:30% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:31% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:31% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:31% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:32% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:32% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:33% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:34% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:34% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:35% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:35% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:36% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:36% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:37% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:37% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:38% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:38% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:39% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:39% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:40% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:40% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:41% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:41% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:42% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:42% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:43% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:43% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:43% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:44% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:44% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:45% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:46% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:46% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:47% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:47% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:48% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:48% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:49% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:49% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:50% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:50% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:51% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:51% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:52% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:52% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:53% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:53% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:54% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:54% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:55% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:55% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:56% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:56% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:57% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:57% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:58% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:58% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:59% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:59% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:60% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:60% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:61% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:61% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:62% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:62% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:63% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:63% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:64% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:64% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:65% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:65% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:65% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:66% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:67% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:67% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:68% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:68% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:69% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:69% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:70% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:70% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:71% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:71% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:72% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:72% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:73% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:73% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:74% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:74% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:75% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:75% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:76% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:76% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:77% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:77% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:78% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:78% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:79% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:79% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:80% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:80% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:81% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:81% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:82% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:82% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:83% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:83% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:84% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:84% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:85% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:85% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:86% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:86% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:87% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:87% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:88% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:88% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:89% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:89% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:90% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:90% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:91% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:91% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:92% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:92% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:93% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:93% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:94% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:94% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:95% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:95% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:96% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:96% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:97% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:97% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:98% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:98% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:99% 
+Conducting the graphical lasso (glasso)....done.                                          
+</code></pre>
+
+<pre><code class="r">glasso.adjacency.confounded=glasso.confounded$path
+glasso.graph.confounded=list()
+for(i in 1:200){
+  glasso.graph.confounded[[i]]=graph.adjacency(glasso.adjacency.confounded[[i]],mode=&quot;undirected&quot;, diag=FALSE)
+}
+
+############ Correct for Confounding (Residuals from PC) ############
+mod=matrix(1,nrow=dim(data.confounded)[1],ncol=1)
+colnames(mod)=&quot;Intercept&quot;
+nsv=num.sv(t(data.confounded),mod)
+
+ss=svd(data.confounded - colMeans(data.confounded))
+grp.est=ss$u[,1]
+data.corrected=data.confounded*0
+for(i in 1:8){
+  data.corrected[,i]=lm(data.confounded[,i] ~ grp.est)$residuals
+}
+
+rownames(data.corrected)=1:(1000*n)
+colnames(data.corrected)=1:8
+
+cor.data.corrected=cor(data.corrected)
+colnames(cor.data.corrected)=rownames(cor.data.corrected)=1:8
+
+
+glasso.corrected.lambda=huge(data.corrected,method=&quot;glasso&quot;,lambda)
+</code></pre>
+
+<pre><code>## Conducting the graphical lasso (glasso) with lossless screening....in progress:0% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:0% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:1% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:1% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:2% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:2% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:3% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:3% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:4% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:4% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:5% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:5% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:6% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:6% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:6% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:7% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:7% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:8% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:8% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:9% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:9% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:10% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:10% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:11% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:12% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:12% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:13% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:13% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:14% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:14% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:15% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:15% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:16% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:16% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:17% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:17% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:18% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:18% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:18% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:19% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:19% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:20% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:20% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:21% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:21% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:22% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:23% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:23% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:24% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:24% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:25% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:25% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:26% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:26% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:27% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:27% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:28% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:28% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:29% 
+Conducting the graphical lasso (glasso) with lossless screening....in progress:29% 
+Conducting the graphical lasso (glasso)....done.                                          
+</code></pre>
+
+<pre><code class="r">glasso.graph.corrected.lambda=list()
+for(i in 1:200){
+  glasso.graph.corrected.lambda[[i]]=graph.adjacency(glasso.corrected.lambda$path[[i]],mode=&quot;undirected&quot;, diag=FALSE)
+
+}
+
+## For a given gene, samples are standard normal
+z.data=data
+for(j in 1:8){
+  mean=mean(data[,j])
+  sd=sd(data[,j])
+  z.data[,j]=(data[,j]-mean)/sd
+}
+
+z.data.confounded=data.confounded
+for(j in 1:8){
+  mean=mean(data.confounded[,j])
+  sd=sd(data.confounded[,j])
+  z.data.confounded[,j]=(data.confounded[,j]-mean)/sd
+}
+
+z.data.corrected=data.corrected
+for(j in 1:8){
+  mean=mean(data.corrected[,j])
+  sd=sd(data.corrected[,j])
+  z.data.corrected[,j]=(data.corrected[,j]-mean)/sd
+}
+</code></pre>
+
+<p>This part generates plots for each figure panel and saves it in a pdf</p>
+
+<pre><code>## png 
+##   2
+</code></pre>
+
+<pre><code>## png 
+##   2
+</code></pre>
+
+<pre><code>## png 
+##   2
+</code></pre>
+
+<pre><code>## png 
+##   2
+</code></pre>
+
+<pre><code>
+The R session information (including the OS info, R version and all
+packages used):
+
+
+```r
+sessionInfo()
+</code></pre>
+
+<pre><code>## R version 3.3.1 (2016-06-21)
+## Platform: x86_64-pc-linux-gnu (64-bit)
+## Running under: CentOS release 6.7 (Final)
+## 
+## locale:
+##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
+##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
+##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
+##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
+##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
+## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
+## 
+## attached base packages:
+## [1] methods   stats     graphics  grDevices utils     datasets  base     
+## 
+## other attached packages:
+##  [1] cowplot_0.8.0           reshape2_1.4.2         
+##  [3] ggplot2_2.2.1           RSkittleBrewer_1.1     
+##  [5] devtools_1.13.3         huge_1.2.7             
+##  [7] igraph_1.1.2            lattice_0.20-35        
+##  [9] Matrix_1.2-11           glasso_1.8             
+## [11] gtable_0.2.0            gridExtra_2.3          
+## [13] sva_3.22.0              genefilter_1.56.0      
+## [15] mgcv_1.8-22             nlme_3.1-131           
+## [17] clusterGeneration_1.3.4 MASS_7.3-47            
+## [19] mvtnorm_1.0-6           knitr_1.17             
+## 
+## loaded via a namespace (and not attached):
+##  [1] splines_3.3.1        colorspace_1.3-2     stats4_3.3.1        
+##  [4] blob_1.1.0           survival_2.41-3      XML_3.98-1.9        
+##  [7] rlang_0.1.2          withr_2.0.0          DBI_0.7             
+## [10] BiocGenerics_0.21.3  bit64_0.9-7          plyr_1.8.4          
+## [13] stringr_1.2.0        munsell_0.4.3        memoise_1.1.0       
+## [16] evaluate_0.10.1      labeling_0.3         Biobase_2.34.0      
+## [19] IRanges_2.8.2        parallel_3.3.1       curl_2.8.1          
+## [22] AnnotationDbi_1.36.2 Rcpp_0.12.13         xtable_1.8-2        
+## [25] scales_0.5.0         S4Vectors_0.12.2     annotate_1.52.1     
+## [28] bit_1.1-12           digest_0.6.12        stringi_1.1.5       
+## [31] grid_3.3.1           tools_3.3.1          bitops_1.0-6        
+## [34] magrittr_1.5         RCurl_1.95-4.8       lazyeval_0.2.0      
+## [37] tibble_1.3.4         RSQLite_2.0          pkgconfig_2.0.1     
+## [40] httr_1.3.1           R6_2.2.2             git2r_0.19.0
+</code></pre>
+
+<pre><code class="r">Sys.time()
+</code></pre>
+
+<pre><code>## [1] &quot;2017-10-13 13:58:52 EDT&quot;
+</code></pre>
+
+</body>
+
+</html>
diff --git a/publication_rmd/simulation_example_fig1/figure1.md b/publication_rmd/simulation_example_fig1/figure1.md
new file mode 100644
index 0000000..abbfc93
--- /dev/null
+++ b/publication_rmd/simulation_example_fig1/figure1.md
@@ -0,0 +1,383 @@
+
+
+
+
+This report was automatically generated with the R package **knitr**
+(version 1.17).
+
+
+```r
+---
+title: "figure_1"
+output:
+  html_document:
+    code_folding: hide
+---
+
+This is a simulation example that shows that confounders and batch effects impact reconstruction of gene co-expression networks. Using this example we also show that true underlying network structure can be reconstructed after principal component correction of gene expression data as described in the paper.
+
+This script generates Figure 1 in the paper -- "Addressing confounding artifacts in reconstruction of gene co-expression networks"
+```
+
+```
+## Error: <text>:8:6: unexpected symbol
+## 7: 
+## 8: This is
+##         ^
+```
+
+```r
+rm(list = ls())
+
+## load libraries
+#library(pcalg)
+library(mvtnorm)
+library(clusterGeneration)
+```
+
+```
+## Loading required package: MASS
+```
+
+```r
+library(sva)
+```
+
+```
+## Loading required package: mgcv
+```
+
+```
+## Loading required package: nlme
+```
+
+```
+## This is mgcv 1.8-22. For overview type 'help("mgcv-package")'.
+```
+
+```
+## Loading required package: genefilter
+```
+
+```
+## Warning: replacing previous import 'stats::sd' by 'BiocGenerics::sd' when
+## loading 'S4Vectors'
+```
+
+```
+## Warning: replacing previous import 'stats::var' by 'BiocGenerics::var' when
+## loading 'S4Vectors'
+```
+
+```
+## Warning: replacing previous import 'stats::sd' by 'BiocGenerics::sd' when
+## loading 'IRanges'
+```
+
+```
+## Warning: replacing previous import 'stats::var' by 'BiocGenerics::var' when
+## loading 'IRanges'
+```
+
+```
+## 
+## Attaching package: 'genefilter'
+```
+
+```
+## The following object is masked from 'package:MASS':
+## 
+##     area
+```
+
+```r
+#library(spacejam)
+library(gridExtra)
+library(gtable)
+library(glasso)
+library(huge)
+```
+
+```
+## Loading required package: Matrix
+```
+
+```
+## Loading required package: lattice
+```
+
+```
+## Loading required package: igraph
+```
+
+```
+## Loading required package: methods
+```
+
+```
+## 
+## Attaching package: 'igraph'
+```
+
+```
+## The following objects are masked from 'package:stats':
+## 
+##     decompose, spectrum
+```
+
+```
+## The following object is masked from 'package:base':
+## 
+##     union
+```
+
+```r
+library(devtools)
+install_github('alyssafrazee/RSkittleBrewer')
+```
+
+```
+## Skipping install of 'RSkittleBrewer' from a github remote, the SHA1 (00881122) has not changed since last install.
+##   Use `force = TRUE` to force installation
+```
+
+```r
+library(RSkittleBrewer)
+tropical = RSkittleBrewer('tropical')
+library(ggplot2)
+library(reshape2)
+library(cowplot)
+```
+
+```
+## 
+## Attaching package: 'cowplot'
+```
+
+```
+## The following object is masked from 'package:ggplot2':
+## 
+##     ggsave
+```
+
+```r
+### Data: 5 features, 10 samples
+p=8
+n=10
+
+V=diag(1,nrow=p,ncol=p)
+V[1,3]=V[3,1]=.35
+V[4,7]=V[7,4]=.3
+V[1,8]=V[8,1]=.3
+V.inv=solve(V)
+
+colnames(V)=rownames(V)=colnames(V.inv)=rownames(V.inv)=paste(1:8)
+
+A.generating=V
+for(i in 1:p){
+  for(j in 1:p){
+    if(abs(V[i,j])>0.05){
+      A.generating[i,j]=1
+    }
+    if(abs(V[i,j])<=0.05){
+      A.generating[i,j]=0
+    }
+  }
+}
+g.generating=graph.adjacency(A.generating,mode="undirected", diag=FALSE,add.colnames=TRUE)
+
+set.seed(4747)
+data=rmvnorm((1000*n),mean=rep(1,p),sigma=V)
+rownames(data)=1:(1000*n)
+colnames(data)=1:8
+
+cor.data=cor(data)
+
+## Graph 
+lambda=seq(1,0.01,length.out=200)
+glasso.unconfounded.lambda=huge(data,lambda,method="glasso")
+```
+
+```
+## Conducting the graphical lasso (glasso) with lossless screening....in progress:0% 
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Conducting the graphical lasso (glasso) with lossless screening....in progress:34% 
Conducting the graphical lasso (glasso)....done.                                          
+```
+
+```r
+glasso.adjacency.unconfounded.lambda=glasso.unconfounded.lambda$path
+glasso.graph.unconfounded.lambda=list()
+
+for(i in 1:200){
+  glasso.graph.unconfounded.lambda[[i]]=graph.adjacency(glasso.adjacency.unconfounded.lambda[[i]],mode="undirected", diag=FALSE)
+}
+
+############ Confounding ############
+data.confounded=data
+grp=rnorm(1000*n)
+for(i in 2:6){
+  data.confounded[,i] = data.confounded[,i] + 50*grp
+}
+
+rownames(data.confounded)=1:(1000*n)
+colnames(data.confounded)=1:8
+
+cor.data.confounded=cor(data.confounded)
+colnames(cor.data.confounded)=rownames(cor.data.confounded)=1:8
+
+colnames(data.confounded)=1:8
+rownames(data.confounded)=1:10000 
+
+glasso.confounded=huge(data.confounded,lambda,method="glasso")
+```
+
+```
+## Conducting the graphical lasso (glasso) with lossless screening....in progress:0% 
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Conducting the graphical lasso (glasso)....done.                                          
+```
+
+```r
+glasso.adjacency.confounded=glasso.confounded$path
+glasso.graph.confounded=list()
+for(i in 1:200){
+  glasso.graph.confounded[[i]]=graph.adjacency(glasso.adjacency.confounded[[i]],mode="undirected", diag=FALSE)
+}
+
+############ Correct for Confounding (Residuals from PC) ############
+mod=matrix(1,nrow=dim(data.confounded)[1],ncol=1)
+colnames(mod)="Intercept"
+nsv=num.sv(t(data.confounded),mod)
+
+ss=svd(data.confounded - colMeans(data.confounded))
+grp.est=ss$u[,1]
+data.corrected=data.confounded*0
+for(i in 1:8){
+  data.corrected[,i]=lm(data.confounded[,i] ~ grp.est)$residuals
+}
+
+rownames(data.corrected)=1:(1000*n)
+colnames(data.corrected)=1:8
+
+cor.data.corrected=cor(data.corrected)
+colnames(cor.data.corrected)=rownames(cor.data.corrected)=1:8
+
+
+glasso.corrected.lambda=huge(data.corrected,method="glasso",lambda)
+```
+
+```
+## Conducting the graphical lasso (glasso) with lossless screening....in progress:0% 
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Conducting the graphical lasso (glasso) with lossless screening....in progress:8% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:8% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:9% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:9% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:10% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:10% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:11% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:12% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:12% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:13% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:13% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:14% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:14% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:15% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:15% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:16% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:16% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:17% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:17% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:18% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:18% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:18% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:19% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:19% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:20% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:20% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:21% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:21% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:22% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:23% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:23% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:24% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:24% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:25% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:25% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:26% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:26% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:27% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:27% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:28% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:28% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:29% 
Conducting the graphical lasso (glasso) with lossless screening....in progress:29% 
Conducting the graphical lasso (glasso)....done.                                          
+```
+
+```r
+glasso.graph.corrected.lambda=list()
+for(i in 1:200){
+  glasso.graph.corrected.lambda[[i]]=graph.adjacency(glasso.corrected.lambda$path[[i]],mode="undirected", diag=FALSE)
+  
+}
+
+## For a given gene, samples are standard normal
+z.data=data
+for(j in 1:8){
+  mean=mean(data[,j])
+  sd=sd(data[,j])
+  z.data[,j]=(data[,j]-mean)/sd
+}
+
+z.data.confounded=data.confounded
+for(j in 1:8){
+  mean=mean(data.confounded[,j])
+  sd=sd(data.confounded[,j])
+  z.data.confounded[,j]=(data.confounded[,j]-mean)/sd
+}
+
+z.data.corrected=data.corrected
+for(j in 1:8){
+  mean=mean(data.corrected[,j])
+  sd=sd(data.corrected[,j])
+  z.data.corrected[,j]=(data.corrected[,j]-mean)/sd
+}
+```
+
+This part generates plots for each figure panel and saves it in a pdf
+
+
+```
+## png 
+##   2
+```
+
+```
+## png 
+##   2
+```
+
+```
+## png 
+##   2
+```
+
+```
+## png 
+##   2
+```
+```
+
+The R session information (including the OS info, R version and all
+packages used):
+
+
+```r
+sessionInfo()
+```
+
+```
+## R version 3.3.1 (2016-06-21)
+## Platform: x86_64-pc-linux-gnu (64-bit)
+## Running under: CentOS release 6.7 (Final)
+## 
+## locale:
+##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
+##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
+##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
+##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
+##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
+## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
+## 
+## attached base packages:
+## [1] methods   stats     graphics  grDevices utils     datasets  base     
+## 
+## other attached packages:
+##  [1] cowplot_0.8.0           reshape2_1.4.2         
+##  [3] ggplot2_2.2.1           RSkittleBrewer_1.1     
+##  [5] devtools_1.13.3         huge_1.2.7             
+##  [7] igraph_1.1.2            lattice_0.20-35        
+##  [9] Matrix_1.2-11           glasso_1.8             
+## [11] gtable_0.2.0            gridExtra_2.3          
+## [13] sva_3.22.0              genefilter_1.56.0      
+## [15] mgcv_1.8-22             nlme_3.1-131           
+## [17] clusterGeneration_1.3.4 MASS_7.3-47            
+## [19] mvtnorm_1.0-6           knitr_1.17             
+## 
+## loaded via a namespace (and not attached):
+##  [1] splines_3.3.1        colorspace_1.3-2     stats4_3.3.1        
+##  [4] blob_1.1.0           survival_2.41-3      XML_3.98-1.9        
+##  [7] rlang_0.1.2          withr_2.0.0          DBI_0.7             
+## [10] BiocGenerics_0.21.3  bit64_0.9-7          plyr_1.8.4          
+## [13] stringr_1.2.0        munsell_0.4.3        memoise_1.1.0       
+## [16] evaluate_0.10.1      labeling_0.3         Biobase_2.34.0      
+## [19] IRanges_2.8.2        parallel_3.3.1       curl_2.8.1          
+## [22] AnnotationDbi_1.36.2 Rcpp_0.12.13         xtable_1.8-2        
+## [25] scales_0.5.0         S4Vectors_0.12.2     annotate_1.52.1     
+## [28] bit_1.1-12           digest_0.6.12        stringi_1.1.5       
+## [31] grid_3.3.1           tools_3.3.1          bitops_1.0-6        
+## [34] magrittr_1.5         RCurl_1.95-4.8       lazyeval_0.2.0      
+## [37] tibble_1.3.4         RSQLite_2.0          pkgconfig_2.0.1     
+## [40] httr_1.3.1           R6_2.2.2             git2r_0.19.0
+```
+
+```r
+Sys.time()
+```
+
+```
+## [1] "2017-10-13 13:58:52 EDT"
+```
+
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