[R] Maintaining specific order when using aggregate or change order on axis

Tue Sep 11 22:00:24 CEST 2012

Hi,
In that case, try this:
#made up data
Coral1<-read.table(text="
Seamount Station  Depth  Pico  Nano Micro Total_Ch
Coral    1401 Surface 0.216 3.270 4.240    7.726
Coral    1401    Fmax 0.359 3.890 4.900    9.149
Coral    1401  Below 0.178 1.360 1.210    2.748
Coral    1402 Surface 0.231 4.140 3.670    8.041
Coral    1402    Fmax 0.863 4.340 3.750    8.953
Coral    1402  Below 0.176 0.386 0.214    0.776
Coral    1401 Surface 0.216 3.270 4.240    7.726
Coral    1401    Shallow 0.359 3.890 4.900    9.149
Coral    1401  Deep 0.278 1.860 1.210    2.748
Coral    1402 Surface 0.331 4.940 3.670    8.041
Coral    1402    Fmax 0.493 4.840 3.750    8.953
Coral    1402  Below 0.186 0.486 0.214    0.776
",sep="",header=TRUE,stringsAsFactors=FALSE)
 Coral2<-with(Coral1 , aggregate(cbind(Pico, Nano, Micro), list(Depth),FUN=mean))
Coral2[order(order(c("Surface","Shallow","Deep","Fmax","Below"))),]
#  Group.1      Pico     Nano    Micro
#5 Surface 0.2485000 3.905000 3.955000
#4 Shallow 0.3590000 3.890000 4.900000
#2    Deep 0.2780000 1.860000 1.210000
#3    Fmax 0.5716667 4.356667 4.133333
#1   Below 0.1800000 0.744000 0.546000
A.K.

________________________________
From: Tinus Sonnekus <tsonnekus at gmail.com>
To: arun <smartpink111 at yahoo.com> 
Sent: Tuesday, September 11, 2012 2:36 PM
Subject: Re: [R] Maintaining specific order when using aggregate or change order on axis

Hi,

Thanks for the reply. I know the order is abit confusing, but here is abit more background info to the depths.

For the various depths the ships's ctd sampled. 

surface = ctd @ surface e.g 5m
shallow = between surface and fmax e.g. 25m
deep = between surface and fmax, but deeper than shallow e.g 50m
fmax = ctd sampled at maximum flouresence  e.g 100m
below = below the fmax e.g. 200m

The problem I can't really assign a specific depth value to each as fmax changed depth depending on location. If fmax was very shallow then "deep" and "shallow" was dropped from the predetermined sampling depths.

Hope this helps explain what I'm trying to do with the ordering of the data.

Thanks for all your help. Been a steep learning curve this last week with R

Shot
Tinus

On Tue, Sep 11, 2012 at 8:16 PM, arun <smartpink111 at yahoo.com> wrote:

Hi,
>The order you mentioned is confusing.  The given data shows depth to be increasing from Below,Surface,Fmax.
>
>This might help you in ordering.
>Coral1<-read.table(text="
>
>Seamount Station  Depth  Pico  Nano Micro Total_Ch
>
>Coral    1401 Surface 0.216 3.270 4.240    7.726
>
>Coral    1401    Fmax 0.359 3.890 4.900    9.149
>
>Coral    1401  Below 0.178 1.360 1.210    2.748
>
>Coral    1402 Surface 0.231 4.140 3.670    8.041
>
>Coral    1402    Fmax 0.863 4.340 3.750    8.953
>
>Coral    1402  Below 0.176 0.386 0.214    0.776
>",sep="",header=TRUE,stringsAsFactors=TRUE)
>
> Coral2<-with(Coral1 , aggregate(cbind(Pico, Nano, Micro), list(Depth),FUN=mean))
> Coral2[order(Coral2$Pico,Coral2$Nano,Coral2$Micro),]
> # Group.1   Pico  Nano Micro
>#1   Below 0.1770 0.873 0.712
>#3 Surface 0.2235 3.705 3.955
>#2    Fmax 0.6110 4.115 4.325
>
>#reverse order
>
> Coral2[rev(order(Coral2$Pico,Coral2$Nano,Coral2$Micro)),]
> # Group.1   Pico  Nano Micro
>#2    Fmax 0.6110 4.115 4.325
>#3 Surface 0.2235 3.705 3.955
>#1   Below 0.1770 0.873 0.712
>
>
>A.K.
>
>
>
>
>
>----- Original Message -----
>From: Tinus Sonnekus <tsonnekus at gmail.com>
>To: r-help at r-project.org
>Cc:
>Sent: Tuesday, September 11, 2012 1:52 PM
>Subject: [R] Maintaining specific order when using aggregate or change order on axis
>
>Hi All,
>
>I'm using the following code to produce some stacked bar graphs.
>
>*setwd("C:\\Users\\Tinus\\Documents\\NMMU\\R\\Seamounts")*
>*SChla <- read.csv("SM_Chla_data.csv")*
>*
>*
>*#Extract mean values from data file*
>*
>*
>*Coral <- SChla[185:223,] #Reduce SChla to Coral only*
>*coral <- with(Coral , aggregate(cbind(Pico, Nano, Micro),
>list(Depth),FUN=mean))*
>*rownames(coral) <- coral[,1] *
>*coral <- t(coral[,-1]) # Remove Station col and transpose*
>
>*barplot(coral, main="Size fractionated Chl a for Coral", *
>* ylab = "Coral", xlim = c(0,8), horiz = TRUE,*
>* xlab = expression ("Chlorophyll a " ~~ (mu*g ~ l^{-1})), *
>* col =c("light green", "green", "dark green"),*
>* legend = rownames(coral))*
>
>Here is the *head(Coral) *before station col removal and t()
>
>    Seamount Station   Depth  Pico  Nano Micro Total_Ch
>185    Coral    1401 Surface 0.216 3.270 4.240    7.726
>186    Coral    1401    Fmax 0.359 3.890 4.900    9.149
>187    Coral    1401   Below 0.178 1.360 1.210    2.748
>188    Coral    1402 Surface 0.231 4.140 3.670    8.041
>189    Coral    1402    Fmax 0.863 4.340 3.750    8.953
>190    Coral    1402   Below 0.176 0.386 0.214    0.776
>
>So I use the same code for the six other seamounts. The depth has
>the following values  surface, shallow, deep, fmax and below . These are in
>order as you go down the water column. The problem is when I use the *coral
><- with(Coral , aggregate(cbind(Pico, Nano, Micro), list(Depth),FUN=mean)) *the
>
>depth values gets stored in ascending values.
>
>head(coral)
>  Group.1      Pico      Nano     Micro
>1   Below 0.1652727 0.8610909 0.7227273
>2    Deep 0.1480000 1.1700000 1.1000000
>3    Fmax 0.3067273 3.1845455 3.2245455
>4 Shallow 0.2617500 1.8242500 1.8637500
>5 Surface 0.1693333 2.7083333 2.7858333
>
>I would like to maintain the order surface, shallow, deep, fmax and below. *Or
>*if there is a way I can rearrange the yaxis in the order surface, shallow,
>
>deep, fmax and below.
>
>Any suggestions?
>
>Thank you
>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 at gmail.com
>
>    [[alternative HTML version deleted]]
>
>______________________________________________
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>PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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>
>

-- 
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 at gmail.com