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.
Thanks for the help and advice.
Tinus
--
M.J. Sonnekus
PhD Candidate (The Phytoplankton of the southern Agulhas Current Large
Marine Ecosystem (ACLME))
Department of Botany
South Campus
Nelson Mandela Metropolitan University
PO Box 77000
Port Elizabeth
South Africa
6031
Cell: 082 080 9638
E-mail: tsonnekus@gmail.com
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Hello, I remember this dataset from not a long time ago. Please use dput() to post your data and do not use formatting to post code. As for the question, though your example is not reproducible (it doesn't run) see http://gallery.r-enthusiasts.com/graph/contour_plot_%3Cbr%3EMaunga_Whau_Volcano,21 Hope this helps, Rui Barradas Em 19-09-2012 16:55, Tinus Sonnekus escreveu:> 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. > > > Thanks for the help and advice. > Tinus >
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