R: levelplot

[bugman]

I am having trouble finishing a level plot in R.

The Y axis is a catergory of substrate and the x axis is the site, with the matrix being the percent of the subtrate type at each site.

My problem (I think) is that I have created a mtrix but R is not recognising the column and row names I have assigned them.

I would like to:

A) plot the y axis with the Column names and xaxis with the row names
B) place the color key under the xaxis.

I don't often use matrices in R (Usually i read them in as csv files). I am guessing this might be much easier to create this plot if I read in my spread sheet as a matrix, but I am not too sure how to go about it.

Any help would be much appreciated? !

see below for code (so far....)




####################
library(lattice)
rock=matrix(c(0,0,0,0,0,0,0,0,10,5,10,5,5,5,15,0,1 0,10,20,20,0,15,15,20,30,0,45,40,30,30,20,15,15,10 ,0,70,10,15,5,0),5,8,
dimnames=list(c("MUR 0931","MUR 28","MUR 0935","MUR 0937","MUR 29"),
c("Clay", "Silt", "Sand", "Gravel", "Pebble", "Cobble", "Boulder", "Bedrock")))
levelplot(rock,xlab="Site", cuts=12.5,ylab="Substrate type" ,colorkey=TRUE, at=c(0,5,10,15,20,25,30,35,40,45,50,55,60,65,70,75 ,80,85,90,95,100), col.regions=(col=gray((30:100)/100)))
axis(1, 1:5, labels=rownames(rock), las=1)
axis(2, 1:8, labels=colnames(rock), las=1)

[TheEcologist]

Originally Posted by bugman

I am having trouble finishing a level plot in R.

A) plot the y axis with the Column names and xaxis with the row names
B) place the color key under the xaxis.

Your code already did A, though I dont really see why you need the axis command.

This works for me:

library(lattice)
rock=matrix(c(0,0,0,0,0,0,0,0,10,5,10,5,5,5,15,0,10,10,20,20,0,15,15,20,30,0,45,40,30,30,20,15,15,10,0,70,10,15,5,0),5,8,
dimnames=list(c("MUR 0931","MUR 28","MUR 0935","MUR 0937","MUR 29"),
c("Clay", "Silt", "Sand", "Gravel", "Pebble", "Cobble", "Boulder", "Bedrock")))
levelplot((rock),xlab="Site", cuts=12.5,ylab="Substrate type" ,colorkey=list(space='bottom'), at=c(0,5,10,15,20,25,30,35,40,45,50,55,60,65,70,75,80,85,90,95,100), col.regions=(col=gray((30:100)/100)))

Originally Posted by bugman

I don't often use matrices in R (Usually i read them in as csv files). I am guessing this might be much easier to create this plot if I read in my spread sheet as a matrix, but I am not too sure how to go about it.

copy & paste your spreadsheet matrix, go into R and type this;

rock=matrix(read.table('clipboard'),dimnames=list( c("MUR 0931","MUR 28","MUR 0935","MUR 0937","MUR 29"),
c("Clay", "Silt", "Sand", "Gravel", "Pebble", "Cobble", "Boulder", "Bedrock")))

[bugman]

Thanks for this!
copy & paste your spreadsheet matrix, go into R and type this;

rock=matrix(read.table('clipboard'),dimnames=list( c("MUR 0931","MUR 28","MUR 0935","MUR 0937","MUR 29"),
c("Clay", "Silt", "Sand", "Gravel", "Pebble", "Cobble", "Boulder", "Bedrock")))[/quote]
Though please excuse my ignorance - where do I paste it? (FYI: I have the matrix as a csv file).
I tried it, but got this warning in return...


#######
In read.table("clipboard") :
incomplete final line found by readTableHeader on 'clipboard'

#################

[TheEcologist]

Originally Posted by bugman

Thanks for this!
#######
In read.table("clipboard") :
incomplete final line found by readTableHeader on 'clipboard'
#################

That looks like an error in your spreadsheet. Make sure your spreadsheet is compatible with R; e.g. no missing entries, no spaces within cells, you dont copy an extra empty row, ect

[TheEcologist]

Originally Posted by bugman

Thanks for this!
#######
In read.table("clipboard") :
incomplete final line found by readTableHeader on 'clipboard'

#################

Also make sure the last thing you do before executing the read.table command is copy your data to the clipboard (crtl + c).. e.g. dont copy your data and then copy your command cause you lose the data... ect ect..

[bugman]

thanks for the tip!