[R] how to make R render plots faster

Abhishek Pratap abhishek.vit at gmail.com
Fri Nov 22 16:59:28 CET 2013

Hi All

We are using R to spit out plots(heatmaps) which are being rendered on
a shiny app (web page). Currently we are facing an issue with the time
it takes R to render a plot taking out the time it takes to do the
computation. Let me show the same through a contrived example. In this
basic test case R takes ~17 seconds to render and save a heatmap file
as png (data computer time is taken out : row and cols clusters are

I am wondering is there a way to reduce the time it takes to render
this plot type by a significant factor. Maybe I am missing on some
other constant computation which can be also taken out of the heatmap

PS: cross posted on stackoverflow


**generate data**

    m1 <- matrix(rnorm(500000,mean=15,sd=4),ncol=100)
    m2 <- matrix(rnorm(500000,mean=30,sd=3),ncol=100)
    m <- cbind(m1,m2)

**basic heat map with all computation**


    user  system elapsed
    29.327   0.637  30.526

**do the clustering out of heatmap function : mainly to test the plot
rendering time**

    > system.time(hcr <- hclust(dist(m)))
       user  system elapsed
      9.992   0.126  10.144
    > system.time(hcc <- hclust(dist(t(m))))
       user  system elapsed
      0.659   0.002   0.662
    > system.time(ddr <- as.dendrogram(hcr))
       user  system elapsed
      0.498   0.010   0.508
    > system.time(ddc <- as.dendrogram(hcc))
       user  system elapsed
      0.011   0.000   0.011

**heatmap rendering time with pre-computed row/col dendogram**

    > system.time(heatmap(m,Rowv=ddr,Colv=ddc))
       user  system elapsed
     16.128   0.558  17.171

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