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R color palettes # Basic grDevice rainbow topo…

R color palettes

  1. Basic grDevice

rainbow()
topo.colors()
terrain.colors()
heat.colors()

my.palette <- terrain.colors(100)
  1. RColoBrewer package
display.brewer.all()

my.palette <- brewer.pal(n, name) For example, my.palette <- brewer.pal(9, "Blues") However, the number of colors is limited up to 9, in most colors. Then use this.

more.color.palette <- colorRampPalette(brewer.pal(9,"Blues"))(100)

http://stackoverflow.com/questions/3832850/color-schemes-in-r
http://www.compbiome.com/2010/12/r-using-rcolorbrewer-to-colour-your.html

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RColorBrewer palette names

RColorBrewer palette names.

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Nice guide for R graphics http blog revolutionanalytics…

Nice guide for R graphics

http://blog.revolutionanalytics.com/2009/01/10-tips-for-making-your-r-graphics-look-their-best.html

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Sometimes R gives the error message Error in…

Sometimes R gives the error message.

Error in X11(d$display, d$width, d$height, d$pointsize, d$gamma, d$colortype,  : 
  unable to start device X11cairo

Here is the fix.

Sys.setenv("DISPLAY"=":0.0")
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Two ways to save a plot in png…

Two ways to save a plot in png.

dev.copy() saves the plot with transparent background while savePlot() with white background.
See the difference.

dev.copy(device = png, file = "devcopy.png")
dev.off()
savePlot(file = "saveplot.png")

Saved by dev.copy()
Saved by savePlot()

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Using discontinuous axis or breaks may not…

Using discontinuous axis or “breaks” may not be a good idea to visualize data.
Instead, use two plots, one with the whole data and another for zoomed data.
However, if the situation is not allowed, there is an R package to do it.
The package plotrix can put breaks or gaps on the axes.

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Using smooth spline in stat scale in ggplot2…

Using smooth.spline in stat_scale in ggplot2

smooth.spline2 <- function(formula, data, ...) { 
  mat <- model.frame(formula, data) 
  smooth.spline(mat[, 2], mat[, 1]) 
} 

predictdf.smooth.spline <- function(model, xseq, se, level) { 
  pred <- predict(model, xseq) 
  data.frame(x = xseq, y = pred$y) 
} 

qplot(mpg, wt, data = mtcars) + geom_smooth(method = "smooth.spline2", se= F)

From: http://groups.google.com/group/ggplot2/browse_thread/thread/149dfa0891fe383a

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Network visualization tool http://gephi …

Network visualization tool
http://gephi.org/

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Print summary results or other outputs o …

Print summary results or other outputs on the R plot

Use capture.output.

summary.text <- paste(capture.output(summary(avg.score.per.pos)), collapse="\n")
mtext(summary.text)
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Getting names while applying sapply or l …

Getting names while applying sapply or lapply in R.
sapply or lapply extract the element without the row name.
So this code does not work.

par(mfrow = c(4,4))
sapply(names(score.avg)
       , function(x) {
           plot(x
                , type = 'l'
              );
           title(main=names(x))      
           })

In order to use the row names while applying sapply or apply,
pass the names of the list to a function and call the values using the names.

par(mfrow = c(4,4))
sapply( Paoua names(score.avg)
       , function(x) {
           xlength <- length(score.avg[[x]]);         
           plot(-499:(xlength-499-1),  http://zikologistes.com/?makakafrancyzka=rencontre-vendee-homme&1dc=f0 score.avg[[x]]
                , type = 'l'
                , xlab='Distance from TSS', ylab='score'
             #   , xlim=c(-100,100)
              );
           title(main=x, cex.main=0.85);
           })