[R] SmoothScatter plot range issue

Henrik Bengtsson hb at stat.berkeley.edu
Mon Sep 22 18:25:26 CEST 2008


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On Mon, Sep 22, 2008 at 7:06 AM, Jason Pare <jay.pare at gmail.com> wrote:
> Hello,
> I am attempting to use smoothScatter to plot a heatmap of locations of
> events in an x-y axis. When I plot the heatmap without passing xlim and ylim
> parameters, it fills the plot area but the perspective is a bit skewed. I
> would like to standardize these plots to a uniform window size that does not
> depend on the range of values in the dataframe. However, when I resize the
> plot using xlim or ylim, there is a light blue background that surrounds the
> immediate area of the data (correspnding to the range of the points listed
> in the dataframe), surrounded by extra white space for the new xlim and ylim
> values I have added. Some of the rings around the datapoints are also cut
> off at the margins.
> I would like to stop the plot from being cut off, and want this light blue
> "range" to extend throughout the entire area of the resized plot. I have
> attempted to add NAs, but it has no effect on expanding this light blue plot
> area. Code is below.
> #### xyz is a dataframe containing two columns with corresponding x and y
> values
> library(geneplotter)
> library(RColorBrewer)
> layout(matrix(1:1, ncol=2, byrow=TRUE))
> smoothScatter(xyz, nrpoints=0, xlim=c(-3,3),
> ylim=c(0,5),colramp=colorRampPalette(c("#f8f8ff", "white",
> "#736AFF", "cyan", "yellow", "#F87431", "#FF7F00", "red",
> "#7E2217")))
> ###END
> Thanks very much for any help,
> Jason
>        [[alternative HTML version deleted]]
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