Ah, I see.
You could try something like this ... create a list of your data at the
outset, then just use the for() loop to create the plots.
Jean
# fake data with two Seamounts ... one with a missing depth
SChla <- structure(list(Seamount = c("Atlantis", "Atlantis", "Atlantis",
"Atlantis", "Atlantis", "Atlantis", "Neptune", "Neptune", "Neptune",
"Neptune", "Neptune"), Station = c(1217L, 1217L, 1217L, 1217L,
1217L, 1225L, 1217L, 1217L, 1217L, 1217L, 1225L), Depth = c("Surface",
"Shallow", "Deep", "Fmax", "Below", "Surface", "Surface", "Shallow",
"Fmax", "Below", "Surface"), Pico = c(0.0639, 0.0305, 0.166,
0.174, 0.0235, 0.0764, 0.0639, 0.0305, 0.174, 0.0235, 0.0764),
Nano = c(0.156, 0.125, 0.356, 0.52, 0.0486, 0.149, 0.156,
0.125, 0.52, 0.0486, 0.149), Micro = c(0.0398, 0.074, 0.0734,
0.183, 0.0242, 0.0333, 0.0398, 0.074, 0.183, 0.0242, 0.0333
), Total_Ch = c(0.2597, 0.2295, 0.5954, 0.877, 0.0963, 0.2587,
0.2597, 0.2295, 0.877, 0.0963, 0.2587), dbar = c(2.082, 24.524,
49.573, 79.595, 199.067, 0.409, 2.082, 24.524, 79.595, 199.067,
0.409)), .Names = c("Seamount", "Station", "Depth", "Pico",
"Nano", "Micro", "Total_Ch", "dbar"), row.names = c("1", "2",
"3", "4", "5", "6", "11", "21", "41", "51", "61"), class = "data.frame")
library(plotrix)
sm.split <- split(SChla, SChla$Seamount)
sm.means <- lapply(sm.split, with, aggregate(cbind(Pico, Nano, Micro,
Total_Ch), list(Depth=Depth), FUN=mean))
colz <- c("light green", "green", "dark green")
for (i in seq(sm.means)) {
sub <- sm.means[[i]]
yy <- t(sub[, 2:4])
dimnames(yy)[[2]] <- sub$Depth
# I used windows() instead of jpeg() so I could quickly see the results on
my PC
windows()
barp(yy, ylim=c(0, max(sub$Total_Ch + 0.1)), col=colz,
xlab="Depth (m)", legend.pos=0.6,
ylab=expression(paste("Chlorophyll ", italic(" a ") ~~ (mu*g ~ l^{-1}))),
names.arg=sub$Depth)
points(sm.means$Total_Ch, pch = 19)
lines(sm.means$Total_Ch)
title(names(sm.means)[i])
legend("topleft", c("Pico", "Nano", "Micro", "Total"), bty="n",
col=c(colz, "black"), pch=c(15, 15, 15, 19), lty=c(0, 0, 0, 1))
}
On Fri, Jun 21, 2013 at 11:23 AM, Tinus Sonnekus <tsonne...@gmail.com>wrote:
> Hi Jean,
>
> Thanks for the help. Yes, it does work but, I need to somehow get rid of
> the "deep" category for the three seamounts with out it. Any ideas?
>
> Regards,
>
>
>
>
> On 21 June 2013 18:16, Adams, Jean <jvad...@usgs.gov> wrote:
>
>> Does it work if you ignore NAs when calculating the max?
>>
>> ylim=c(0,max(sm.mean$Total_Ch + 0.1, na.rm=TRUE))
>>
>> Jean
>>
>>
>> On Fri, Jun 21, 2013 at 7:30 AM, Tinus Sonnekus <tsonne...@gmail.com>wrote:
>>
>>> Hi all,
>>>
>>> So this code works for three of the six seamounts. The problem I am
>>> encountering is the fact that some of the seamounts doesn't have all the
>>> depth categories (i.e missing the deep category) and thus gives me this
>>> error "Error in plot.window(...) : need finite 'ylim' values."
>>>
>>> How can I fix this so that if a depth category is missing that it won't
>>> result in an error. If I change ylim=c(0,max(sm.mean$Total_Ch + 0.1)), to
>>> something like this ylim=c(0,6)), then it works but the I don't like
>>> scale.
>>>
>>> Please help and thank you.
>>>
>>> > head(SChla)
>>> Seamount Station Depth Pico Nano Micro Total_Ch dbar
>>> 1 Atlantis 1217 Surface 0.0639 0.1560 0.0398 0.2597 2.082
>>> 2 Atlantis 1217 Shallow 0.0305 0.1250 0.0740 0.2295 24.524
>>> 3 Atlantis 1217 Deep 0.1660 0.3560 0.0734 0.5954 49.573
>>> 4 Atlantis 1217 Fmax 0.1740 0.5200 0.1830 0.8770 79.595
>>> 5 Atlantis 1217 Below 0.0235 0.0486 0.0242 0.0963 199.067
>>> 6 Atlantis 1225 Surface 0.0764 0.1490 0.0333 0.2587 0.409
>>>
>>>
>>> # Get the unique seamounts
>>> as.character(unique(SChla$Seamount))
>>> sm <- as.character(unique(SChla$Seamount))
>>>
>>> for ( i in sm[1:6]) {
>>> SM.mean <- subset(SChla,Seamount==i,
>>> select=c(Seamount, Station, Depth, Pico, Nano, Micro, Total_Ch))
>>> sm.mean <- with(SM.mean, aggregate(cbind(Pico, Nano, Micro, Total_Ch),
>>> list(Depth),FUN=mean))
>>> sm.mean <-
>>> sm.mean[order(order(c("Surface","Shallow","Deep","Fmax","Below"))),]
>>> yy <- matrix(c(sm.mean$Pico,sm.mean$Nano, sm.mean$Micro),5,3,byrow=FALSE,
>>> dimnames = list(c("Below", "Deep", "Fmax", "Shallow", "Surface"),
>>> c("Pico", "Nano", "Micro")))
>>> yy <- t(yy)
>>>
>>> jpeg(filename = paste(i,"
>>> Seamount.jpg"),res=300,width=15,height=10,units="cm")
>>>
>>> barp(yy , ylim=c(0,max(sm.mean$Total_Ch + 0.1)), col=c("light
>>> green","green","dark green"),
>>> xlab="Depth (m)",
>>> legend.pos = 0.6,
>>> ylab= expression (paste("Chlorophyll ", italic(" a ") ~~ (mu*g ~
>>> l^{-1}))),,
>>> names.arg=c("Surface","Shallow","Deep","Fmax","Below"))
>>> points(sm.mean$Total_Ch, pch = 19)
>>> lines(sm.mean$Total_Ch)
>>> title(i)
>>> legend("topleft",c("Pico","Nano","Micro", "Total"),bty="n",
>>> col=c("light green","green","dark green","black"),
>>> pch=c(15,15,15,19,-1),
>>> lty = c(0,0,0,1))
>>> }
>>> dev.off()
>>>
>>>
>>>
>>> Regards,
>>> 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: tsonne...@gmail.com
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> ______________________________________________
>>> R-help@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide
>>> http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>
>>
>
>
> --
> 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: tsonne...@gmail.com
>
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