R help - Sep 2008 - SmoothScatter plot range issue

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]]

Hi,

Bioconductor.org is the home of the geneplotter package.  You get a
quicker response if you ask there.

/Henrik

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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