automation

R/functions.R

@@ -970,14 +970,14 @@ grid <- function(x,y,xlim=NULL,ylim=NULL,n=10){
             M[i,j] <- sum(x >= xc[i] & x <= xc[i+1] & y <= yc[j] & y >= yc[j+1])
         }
     }
-    M <- M/(1.5*max(M))
+    M <- sqrt(M)/(1.25*sqrt(max(M)))
     
     # fill plot
     for(i in seq_len(n)){
         for(j in seq_len(n)){
             graphics::polygon(x=c(xc[i],xc[i],xc[i+1],xc[i+1]),
                               y=c(yc[j],yc[j+1],yc[j+1],yc[j]),
-                              col=gray(level=1-M[i,j]))
+                              col=gray(level=1-M[i,j]),border=NA)
         }
     }
     graphics::segments(x0=xc,y0=ylim[1],y1=ylim[2],col="white")

docs/articles/code.html

@@ -188,15 +188,17 @@
 <a class="sourceLine" id="cb6-7" data-line-number="7">    b &lt;-<span class="st"> </span>pvalue; pvalue &lt;-<span class="st"> </span><span class="ot">NA</span></a>
 <a class="sourceLine" id="cb6-8" data-line-number="8"></a>
 <a class="sourceLine" id="cb6-9" data-line-number="9">    names &lt;-<span class="st"> </span><span class="kw">intersect</span>(<span class="kw">rownames</span>(a),<span class="kw">rownames</span>(b))</a>
-<a class="sourceLine" id="cb6-10" data-line-number="10">    <span class="kw">plot</span>(<span class="kw">jitter</span>(<span class="op">-</span><span class="kw">log</span>(a[names,sel])),<span class="kw">jitter</span>(<span class="op">-</span><span class="kw">log</span>(b[names,sel])))</a>
-<a class="sourceLine" id="cb6-11" data-line-number="11">    cor[chr] &lt;-<span class="st"> </span>stats<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/stats/topics/cor">cor</a></span>(a[names,sel],b[names,sel],<span class="dt">method=</span><span class="st">"spearman"</span>)</a>
-<a class="sourceLine" id="cb6-12" data-line-number="12"></a>
-<a class="sourceLine" id="cb6-13" data-line-number="13">    a &lt;-<span class="st"> </span>stats<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/stats/topics/p.adjust">p.adjust</a></span>(a[names,sel])<span class="op">&lt;</span><span class="fl">0.05</span></a>
-<a class="sourceLine" id="cb6-14" data-line-number="14">    b &lt;-<span class="st"> </span>stats<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/stats/topics/p.adjust">p.adjust</a></span>(b[names,sel])<span class="op">&lt;</span><span class="fl">0.05</span></a>
-<a class="sourceLine" id="cb6-15" data-line-number="15">    <span class="kw">print</span>(<span class="kw">paste0</span>(<span class="st">"chr"</span>,chr))</a>
-<a class="sourceLine" id="cb6-16" data-line-number="16">    <span class="kw">print</span>(<span class="kw">table</span>(a,b))</a>
-<a class="sourceLine" id="cb6-17" data-line-number="17">    chisq[chr] &lt;-<span class="st"> </span>stats<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/stats/topics/chisq.test">chisq.test</a></span>(<span class="kw">table</span>(a,b))<span class="op">$</span>p.value</a>
-<a class="sourceLine" id="cb6-18" data-line-number="18">}</a></code></pre></div>
+<a class="sourceLine" id="cb6-10" data-line-number="10">    <span class="co"># plot(jitter(-log(a[names,sel])),jitter(-log(b[names,sel])))</span></a>
+<a class="sourceLine" id="cb6-11" data-line-number="11">    spliceQTL<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/spliceQTL/topics/grid">grid</a></span>(<span class="dt">x=</span><span class="op">-</span><span class="kw">log</span>(a[names,sel]),<span class="dt">y=</span><span class="op">-</span><span class="kw">log</span>(b[names,sel]),<span class="dt">n=</span><span class="dv">20</span>)</a>
+<a class="sourceLine" id="cb6-12" data-line-number="12">    </a>
+<a class="sourceLine" id="cb6-13" data-line-number="13">    cor[chr] &lt;-<span class="st"> </span>stats<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/stats/topics/cor">cor</a></span>(a[names,sel],b[names,sel],<span class="dt">method=</span><span class="st">"spearman"</span>)</a>
+<a class="sourceLine" id="cb6-14" data-line-number="14"></a>
+<a class="sourceLine" id="cb6-15" data-line-number="15">    a &lt;-<span class="st"> </span>stats<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/stats/topics/p.adjust">p.adjust</a></span>(a[names,sel])<span class="op">&lt;</span><span class="fl">0.05</span></a>
+<a class="sourceLine" id="cb6-16" data-line-number="16">    b &lt;-<span class="st"> </span>stats<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/stats/topics/p.adjust">p.adjust</a></span>(b[names,sel])<span class="op">&lt;</span><span class="fl">0.05</span></a>
+<a class="sourceLine" id="cb6-17" data-line-number="17">    <span class="kw">print</span>(<span class="kw">paste0</span>(<span class="st">"chr"</span>,chr))</a>
+<a class="sourceLine" id="cb6-18" data-line-number="18">    <span class="kw">print</span>(<span class="kw">table</span>(a,b))</a>
+<a class="sourceLine" id="cb6-19" data-line-number="19">    chisq[chr] &lt;-<span class="st"> </span>stats<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/stats/topics/chisq.test">chisq.test</a></span>(<span class="kw">table</span>(a,b))<span class="op">$</span>p.value</a>
+<a class="sourceLine" id="cb6-20" data-line-number="20">}</a></code></pre></div>
 <!--
 #wait <- TRUE
 #while(wait){
@@ -205,44 +207,6 @@
 #}
 memory and CPU usage Linux: htop
 -->
-<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1">grid &lt;-<span class="st"> </span><span class="cf">function</span>(x,y,<span class="dt">xlim=</span><span class="ot">NULL</span>,<span class="dt">ylim=</span><span class="ot">NULL</span>,<span class="dt">n=</span><span class="dv">10</span>){</a>
-<a class="sourceLine" id="cb7-2" data-line-number="2">    <span class="co"># open plot</span></a>
-<a class="sourceLine" id="cb7-3" data-line-number="3">    <span class="cf">if</span>(<span class="kw">is.null</span>(xlim)){xlim &lt;-<span class="st"> </span><span class="kw">range</span>(x)}</a>
-<a class="sourceLine" id="cb7-4" data-line-number="4">    <span class="cf">if</span>(<span class="kw">is.null</span>(ylim)){ylim &lt;-<span class="st"> </span><span class="kw">range</span>(y)}</a>
-<a class="sourceLine" id="cb7-5" data-line-number="5">    graphics<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/graphics/topics/frame">plot.new</a></span>()</a>
-<a class="sourceLine" id="cb7-6" data-line-number="6">    graphics<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/graphics/topics/plot.window">plot.window</a></span>(<span class="dt">xlim=</span>xlim,<span class="dt">ylim=</span>ylim)</a>
-<a class="sourceLine" id="cb7-7" data-line-number="7">    graphics<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/graphics/topics/box">box</a></span>()</a>
-<a class="sourceLine" id="cb7-8" data-line-number="8">    graphics<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/graphics/topics/axis">axis</a></span>(<span class="dt">side=</span><span class="dv">1</span>)</a>
-<a class="sourceLine" id="cb7-9" data-line-number="9">    graphics<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/graphics/topics/axis">axis</a></span>(<span class="dt">side=</span><span class="dv">2</span>)</a>
-<a class="sourceLine" id="cb7-10" data-line-number="10">    </a>
-<a class="sourceLine" id="cb7-11" data-line-number="11">    <span class="co"># density</span></a>
-<a class="sourceLine" id="cb7-12" data-line-number="12">    xc &lt;-<span class="st"> </span><span class="kw">seq</span>(<span class="dt">from=</span>xlim[<span class="dv">1</span>],<span class="dt">to=</span>xlim[<span class="dv">2</span>],<span class="dt">length.out=</span>n<span class="op">+</span><span class="dv">1</span>)</a>
-<a class="sourceLine" id="cb7-13" data-line-number="13">    yc &lt;-<span class="st"> </span><span class="kw">seq</span>(<span class="dt">from=</span>ylim[<span class="dv">2</span>],<span class="dt">to=</span>ylim[<span class="dv">1</span>],<span class="dt">length.out=</span>n<span class="op">+</span><span class="dv">1</span>)</a>
-<a class="sourceLine" id="cb7-14" data-line-number="14">    M &lt;-<span class="st"> </span><span class="kw">matrix</span>(<span class="kw">integer</span>(),<span class="dt">nrow=</span>n,<span class="dt">ncol=</span>n)</a>
-<a class="sourceLine" id="cb7-15" data-line-number="15">    <span class="cf">for</span>(i <span class="cf">in</span> <span class="kw">seq_len</span>(n)){</a>
-<a class="sourceLine" id="cb7-16" data-line-number="16">        <span class="cf">for</span>(j <span class="cf">in</span> <span class="kw">seq_len</span>(n)){</a>
-<a class="sourceLine" id="cb7-17" data-line-number="17">            M[i,j] &lt;-<span class="st"> </span><span class="kw">sum</span>(x <span class="op">&gt;=</span><span class="st"> </span>xc[i] <span class="op">&amp;</span><span class="st"> </span>x <span class="op">&lt;=</span><span class="st"> </span>xc[i<span class="op">+</span><span class="dv">1</span>] <span class="op">&amp;</span><span class="st"> </span>y <span class="op">&lt;=</span><span class="st"> </span>yc[j] <span class="op">&amp;</span><span class="st"> </span>y <span class="op">&gt;=</span><span class="st"> </span>yc[j<span class="op">+</span><span class="dv">1</span>])</a>
-<a class="sourceLine" id="cb7-18" data-line-number="18">        }</a>
-<a class="sourceLine" id="cb7-19" data-line-number="19">    }</a>
-<a class="sourceLine" id="cb7-20" data-line-number="20">    M &lt;-<span class="st"> </span>M<span class="op">/</span>(<span class="fl">1.5</span><span class="op">*</span><span class="kw">max</span>(M))</a>
-<a class="sourceLine" id="cb7-21" data-line-number="21">    </a>
-<a class="sourceLine" id="cb7-22" data-line-number="22">    <span class="co"># fill plot</span></a>
-<a class="sourceLine" id="cb7-23" data-line-number="23">    <span class="cf">for</span>(i <span class="cf">in</span> <span class="kw">seq_len</span>(n)){</a>
-<a class="sourceLine" id="cb7-24" data-line-number="24">        <span class="cf">for</span>(j <span class="cf">in</span> <span class="kw">seq_len</span>(n)){</a>
-<a class="sourceLine" id="cb7-25" data-line-number="25">            graphics<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/graphics/topics/polygon">polygon</a></span>(<span class="dt">x=</span><span class="kw">c</span>(xc[i],xc[i],xc[i<span class="op">+</span><span class="dv">1</span>],xc[i<span class="op">+</span><span class="dv">1</span>]),</a>
-<a class="sourceLine" id="cb7-26" data-line-number="26">                              <span class="dt">y=</span><span class="kw">c</span>(yc[j],yc[j<span class="op">+</span><span class="dv">1</span>],yc[j<span class="op">+</span><span class="dv">1</span>],yc[j]),</a>
-<a class="sourceLine" id="cb7-27" data-line-number="27">                              <span class="dt">col=</span><span class="kw">gray</span>(<span class="dt">level=</span><span class="dv">1</span><span class="op">-</span>M[i,j]))</a>
-<a class="sourceLine" id="cb7-28" data-line-number="28">        }</a>
-<a class="sourceLine" id="cb7-29" data-line-number="29">    }</a>
-<a class="sourceLine" id="cb7-30" data-line-number="30">    graphics<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/graphics/topics/segments">segments</a></span>(<span class="dt">x0=</span>xc,<span class="dt">y0=</span>ylim[<span class="dv">1</span>],<span class="dt">y1=</span>ylim[<span class="dv">2</span>],<span class="dt">col=</span><span class="st">"white"</span>)</a>
-<a class="sourceLine" id="cb7-31" data-line-number="31">    graphics<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/graphics/topics/segments">segments</a></span>(<span class="dt">x0=</span>xlim[<span class="dv">1</span>],<span class="dt">x1=</span>xlim[<span class="dv">2</span>],<span class="dt">y0=</span>yc,<span class="dt">col=</span><span class="st">"white"</span>)</a>
-<a class="sourceLine" id="cb7-32" data-line-number="32">    graphics<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/graphics/topics/points">points</a></span>(<span class="dt">x=</span>x,<span class="dt">y=</span>y,<span class="dt">pch=</span><span class="dv">16</span>,<span class="dt">cex=</span><span class="fl">0.5</span>)</a>
-<a class="sourceLine" id="cb7-33" data-line-number="33">    </a>
-<a class="sourceLine" id="cb7-34" data-line-number="34">}</a>
-<a class="sourceLine" id="cb7-35" data-line-number="35"></a>
-<a class="sourceLine" id="cb7-36" data-line-number="36">x &lt;-<span class="st"> </span>stats<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/stats/topics/Beta">rbeta</a></span>(<span class="dt">n=</span><span class="dv">100</span>,<span class="dt">shape1=</span><span class="fl">0.4</span>,<span class="dt">shape2=</span><span class="fl">0.5</span>)</a>
-<a class="sourceLine" id="cb7-37" data-line-number="37">y &lt;-<span class="st"> </span>stats<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/stats/topics/Beta">rbeta</a></span>(<span class="dt">n=</span><span class="dv">100</span>,<span class="dt">shape1=</span><span class="fl">0.2</span>,<span class="dt">shape2=</span><span class="fl">0.5</span>)</a>
-<a class="sourceLine" id="cb7-38" data-line-number="38"><span class="kw"><a href="../reference/grid.html">grid</a></span>(x,y,<span class="dt">xlim=</span><span class="kw">c</span>(<span class="dv">0</span>,<span class="dv">1</span>),<span class="dt">ylim=</span><span class="kw">c</span>(<span class="dv">0</span>,<span class="dv">1</span>),<span class="dt">n=</span><span class="dv">10</span>)</a></code></pre></div>
   </div>
 
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">

vignettes/code.Rmd

@@ -120,7 +120,7 @@ On the virtual machine, execute this chunk to compare the results between the Ge
 
 ```{r,eval=FALSE}
 cor <- chisq <- rep(NA,length=22)
-for(chr in 22:1){
+for(chr in 1){
     sel <- "rho=1"
     load(file.path(path,paste0("pval.Geuvadis.chr",chr,".RData")))
     a <- pvalue; pvalue <- NA
@@ -128,7 +128,9 @@ for(chr in 22:1){
     b <- pvalue; pvalue <- NA
 
     names <- intersect(rownames(a),rownames(b))
-    plot(jitter(-log(a[names,sel])),jitter(-log(b[names,sel])))
+    # plot(jitter(-log(a[names,sel])),jitter(-log(b[names,sel])))
+    spliceQTL::grid(x=-log(a[names,sel]),y=-log(b[names,sel]),n=20)
+    
     cor[chr] <- stats::cor(a[names,sel],b[names,sel],method="spearman")
 
     a <- stats::p.adjust(a[names,sel])<0.05
@@ -147,50 +149,3 @@ for(chr in 22:1){
 #}
 memory and CPU usage Linux: htop
 -->
-
-
-
-```{r plot function,eval=FALSE}
-grid <- function(x,y,xlim=NULL,ylim=NULL,n=10){
-    # open plot
-    if(is.null(xlim)){xlim <- range(x)}
-    if(is.null(ylim)){ylim <- range(y)}
-    graphics::plot.new()
-    graphics::plot.window(xlim=xlim,ylim=ylim)
-    graphics::box()
-    graphics::axis(side=1)
-    graphics::axis(side=2)
-    
-    # density
-    xc <- seq(from=xlim[1],to=xlim[2],length.out=n+1)
-    yc <- seq(from=ylim[2],to=ylim[1],length.out=n+1)
-    M <- matrix(integer(),nrow=n,ncol=n)
-    for(i in seq_len(n)){
-        for(j in seq_len(n)){
-            M[i,j] <- sum(x >= xc[i] & x <= xc[i+1] & y <= yc[j] & y >= yc[j+1])
-        }
-    }
-    M <- M/(1.5*max(M))
-    
-    # fill plot
-    for(i in seq_len(n)){
-        for(j in seq_len(n)){
-            graphics::polygon(x=c(xc[i],xc[i],xc[i+1],xc[i+1]),
-                              y=c(yc[j],yc[j+1],yc[j+1],yc[j]),
-                              col=gray(level=1-M[i,j]))
-        }
-    }
-    graphics::segments(x0=xc,y0=ylim[1],y1=ylim[2],col="white")
-    graphics::segments(x0=xlim[1],x1=xlim[2],y0=yc,col="white")
-    graphics::points(x=x,y=y,pch=16,cex=0.5)
-    
-}
-
-x <- stats::rbeta(n=100,shape1=0.4,shape2=0.5)
-y <- stats::rbeta(n=100,shape1=0.2,shape2=0.5)
-grid(x,y,xlim=c(0,1),ylim=c(0,1),n=10)
-
-
-
-```
-