On Sep 19, 2012, at 8:55 AM, Tinus Sonnekus wrote:
> Hi All,
>
> I am trying to reproduce this using R instead.
>
> [image: Full-size image (38 K)]
>
>
> I tried using the following code
>
> *SChla <- read.csv("SM_Chla_data.csv")*
>
> *Atlantis <- SChla[16:66,]*
> *head(Atlantis)*
> *
> *
> Seamount Station Depth Pico Nano Micro Total_Ch dbar Latitude
> Longitud
> 16 Atlantis 1217 Surface 0.0639 0.1560 0.0398 0.2597 2.082 -32.71450
> 57.29733
> 17 Atlantis 1217 Shallow 0.0305 0.1250 0.0740 0.2295 24.524 -32.71450
> 57.29733
> 18 Atlantis 1217 Deep 0.1660 0.3560 0.0734 0.5954 49.573 -32.71450
> 57.29733
> 19 Atlantis 1217 Fmax 0.1740 0.5200 0.1830 0.8770 79.595 -32.71450
> 57.29733
> 20 Atlantis 1217 Below 0.0235 0.0486 0.0242 0.0963 199.067 -32.71450
> 57.29733
> 21 Atlantis 1225 Surface 0.0764 0.1490 0.0333 0.2587 0.409 -32.71133
> 57.27150
>
> *# Obtaining longitude and depth data*
> *Long <- SMfrac[,6]*
> *dbar <- -SMfrac[,5] #reverse depth*
> *
> *
> *#converting data to percentage of total chl a*
> *
> *
> *picoFrac <- Atlantis$Pico/Atlantis$Total_Ch*100*
> *nanoFrac <- Atlantis$Nano/Atlantis$Total_Ch*100*
> *microFrac <- Atlantis$Micro/Atlantis$Total_Ch*100*
> *
> *
> *
> *
> *library(akima)*
> *
> *
> *par(mfrow = c(3,1)) *
> *
> *
> *contour(interp(Long, dbar, picoFrac),nlevels = 6,*
> * xlab ="Longitude", main= "Pico", *
> * ylab ="Depth", ylim = c(-200,0), method = "simple",*
> * col = "light green")*
> *
> *
> *contour(interp(Long, dbar, nanoFrac), nlevels = 6,*
> * xlab ="Longitude", main= "Nano",*
> * ylab ="Depth",ylim = c(-200,0), method = "simple",*
> * col = "green")*
> *
> *
> *contour(interp(Long, dbar, microFrac),nlevels = 6,*
> * xlab ="Longitude", main= "Micro",*
> * ylab ="Depth",ylim = c(-200,0), *
> * lylab ="Depth", method = "simple",*
> * col = "dark green")*
>
> I can get the contours plotted. Not sure if this is 100 % correct but it
> looks as expected. Can you guys please help me to add/display my data
> points. I would also like to fill the contours in grayscale/colour (e.g.
> levels 0, 20, 40, 60, 80. 100 %) and add a legend to the graph. As of yet I
> haven't tried to figure out how to add the stations as a secondary axis to
> the plot.
>
Why wouldn't you just use the points() function after each contour?
--
David.
David Winsemius, MD
Alameda, CA, USA
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