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

[arun]

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

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