R help - Jun 2011 - scatterplot3d - help assign colors based on multiple conditions

Hi 

I am relatively new to R and am trying to figure out to plot 3d scatter plot
using defined colors based on x-axis and y-axis values.  Right now in the code
below, I assign colors based on certain values in the names of the x-axis.  Now
if I want to extend the condition to assign a color based on the names of both
x-axis and y-axis values, what should I be doing? Any help or ideas would be
greatly appreciated.

For e.g. in my 3 column matrix below, if I want to assign "red" to all
the values whose first column and second column contain
"Anterior_nares" and  assign black to any other combination.

Thanks!
Karthik

library(scatterplot3d)

chd1=read.table(file="test.out", header=F, sep="\t")
col=as.vector(chd1[,1])
xlabels=as.vector(chd1[,1])
ylabels=as.vector(chd1[,2])

mycols<-c("red","blue","green","chocolate","orange",
"brown")
col[grep("_Stool", xlabels) ]<-mycols[1]
#col[grep("_Stool", xlabels) && grep("_Stool",
ylabels) ]<-mycols[1]
col[grep("_Tongue_dorsum", xlabels) ]<-mycols[2]
col[grep("_Posterior_fornix", xlabels) ]<-mycols[3]
col[grep("_Anterior_nares", xlabels) ]<-mycols[4]
col[grep("_Buccal_mucosa", xlabels) ]<-mycols[5]
col[grep("_Supragingival_plaque", xlabels) ]<-mycols[6]


png(file="3dplot_test.png", w=700,h=700)

scatterplot3d(chd1[, 1], chd1[, 2], chd1[, 3], main="test",
xlab="sample", ylab="sample", zlab="kmers",
color=col,type="p")
dev.off ()


my test.out matrix looks something like this:

A011132_Anterior_nares	A011263_Anterior_nares	50130
A011132_Anterior_nares	A011397_Stool	34748
A011132_Anterior_nares	A012291_Tongue	40859
A011132_Anterior_nares	A012663_Buccal_mucosa	76213
A011132_Anterior_nares	A013155_Anterior_nares	36841
A011132_Anterior_nares	A013269_Anterior_nares	45619
A011132_Anterior_nares	A013637_Anterior_nares	56995
	[[alternative HTML version deleted]]

On 09.06.2011 16:51, Karthik Kota wrote:
> Hi
>
> I am relatively new to R and am trying to figure out to plot 3d scatter
plot using defined colors based on x-axis and y-axis values.  Right now in the
code below, I assign colors based on certain values in the names of the x-axis. 
Now if I want to extend the condition to assign a color based on the names of
both x-axis and y-axis values, what should I be doing? Any help or ideas would
be greatly appreciated.
>
> For e.g. in my 3 column matrix below, if I want to assign "red"
to all the values whose first column and second column contain
"Anterior_nares" and  assign black to any other combination.

Both question and answer are not really scatterplot3d related: You 
probably want

col <- ifelse(grepl("_Anterior_nares", xlabels) & 
grepl("_Anterior_nares", ylabels), "red", "black")

Best,
Uwe Ligges


> Thanks!
> Karthik
>
> library(scatterplot3d)
>
> chd1=read.table(file="test.out", header=F, sep="\t")
> col=as.vector(chd1[,1])
> xlabels=as.vector(chd1[,1])
> ylabels=as.vector(chd1[,2])
>
>
mycols<-c("red","blue","green","chocolate","orange",
"brown")
> col[grep("_Stool", xlabels) ]<-mycols[1]
> #col[grep("_Stool", xlabels)&&  grep("_Stool",
ylabels) ]<-mycols[1]
> col[grep("_Tongue_dorsum", xlabels) ]<-mycols[2]
> col[grep("_Posterior_fornix", xlabels) ]<-mycols[3]
> col[grep("_Anterior_nares", xlabels) ]<-mycols[4]
> col[grep("_Buccal_mucosa", xlabels) ]<-mycols[5]
> col[grep("_Supragingival_plaque", xlabels) ]<-mycols[6]
>
>
> png(file="3dplot_test.png", w=700,h=700)
>
> scatterplot3d(chd1[, 1], chd1[, 2], chd1[, 3], main="test",
xlab="sample", ylab="sample", zlab="kmers",
color=col,type="p")
> dev.off ()
>
>
> my test.out matrix looks something like this:
>
> A011132_Anterior_nares	A011263_Anterior_nares	50130
> A011132_Anterior_nares	A011397_Stool	34748
> A011132_Anterior_nares	A012291_Tongue	40859
> A011132_Anterior_nares	A012663_Buccal_mucosa	76213
> A011132_Anterior_nares	A013155_Anterior_nares	36841
> A011132_Anterior_nares	A013269_Anterior_nares	45619
> A011132_Anterior_nares	A013637_Anterior_nares	56995
> 	[[alternative HTML version deleted]]
>
> ______________________________________________
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> 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.

Thanks! That did the trick. 


On Jun 10, 2011, at 3:16 AM, Jim Lemon wrote:
> On 06/10/2011 06:40 AM, Karthik Kota wrote:
>> Thanks a lot! This is very helpful.
>> 
>> If I have to extend this to one more condition say assign
"blue" if both the corresponding labels have
"_Tongue_dorsum", is there a straight forward function. Doing
something like below is overriding the colors assigned by the first statement.
>> 
>> col<- ifelse(grepl("_Anterior_nares", xlabels)& 
grepl("_Anterior_nares", ylabels), "red", "black")
>> col<- ifelse(grepl("_Tongue_dorsum", xlabels)& 
grepl("_Tongue_dorsum", ylabels), "blue", "black")
>> 
> Hi Karthik,
> Your problem is that you are assigning all of the values to "col"
twice. If you reverse the order of the statements you will get the red/black
color set. Try this:
> 
> col<-rep("black",dim(cdh1)[1])
> col[grepl("_Anterior_nares", xlabels) &
> grepl("_Anterior_nares", ylabels)]<-"red"
> col[grepl("_Tongue_dorsum", xlabels) &
> grepl("_Tongue_dorsum", ylabels)]<-"blue"
> 
> If your two conditions specify disjunct sets, that is, no case satisfies
both conditions, you should have the correct vector of colors.
> 
> Jim