[R] wrong labels and colors of points in graph/plot

David Winsemius dwinsemius at comcast.net
Thu Jun 4 19:38:15 CEST 2009 

Was not able to find NCStats on CRAN or BioConductor repositories. You  
are wasting our (or mine at any rate) time by giving us dead ends.

You have been bitten by the "factor snake in the grass". Color should  
be text rather than a factor if you want the desired results.

See if this is illuminating and eventually helpful:
 > str(coefficient2)
'data.frame':	26 obs. of  11 variables:
  $ site_no                  : num  29 10 17 18 19 25 9 33 37 41 ...
  $ intercept                : num  0.603 2.767 3.6 1.86 2.753 ...
  $ slope                    : num  0.912 0.867 0.841 0.99 0.911 ...
  $ average_height           : num  90.4 2096.2 990 1950 2184 ...
  $ average_crown_length     : num  NA 1066 592 645 795 ...
  $ average_dbh              : num  11.8 271.2 105.1 169.2 220.9 ...
  $ average_age              : num  NA 80.3 19.3 50.9 68.2 ...
  $ average_BM_branches      : num  NA 66649 12679 11246 38049 ...
  $ average_BM_leaves_needles: num  2.28 31051.41 7727.07 9322.6  
27112.2 ...
  $ average_BM_total         : num  36.7 538194.3 62332.9 163137.2  
339177.5 ...
  $ color                    : Factor w/ 4 levels  
"violet","yellow",..: 1 2 2 2 2 2 1 3 1 1 ...
 >  as.character(coefficient2$color)
  [1] "violet" "yellow" "yellow" "yellow" "yellow" "yellow" "violet"  
"black"  "violet" "violet" "black"
[12] "yellow" "violet" "yellow" "violet" "violet" "violet" "yellow"  
"violet" "violet" "black"  "green"
[23] "green"  "green"  "green"  "green"
 >  coefficient2$color <- as.character(coefficient2$color)

Now do your plots....

-- 
David

On Jun 4, 2009, at 12:54 PM, katharina wrote:

>
> sorry, the attachment can be found here for download:
> http://www.wzw.tum.de/waldinventur/fileadmin/coefficient2.RData
>
>
>
> katharina wrote:
>>
>> Hi there,
>>
>> I trying to solve this problem for the whole day not going anywhere,
>> so I  really hope maybe somebody can help
>> me in this community...
>> I've got an object coefficient2 which I want to plot in differerent
>> ways, with colors and labels added to the points,
>> but somehow there seems to be a problem if a value is NA within the
>> independent variable, resulting in false labels and false colors for
>> the points.
>>
>> plot(coefficient2$intercept ~ coefficient2$average_height,
>> main="intercepts ::: height", ylab="intercepts", xlab="average height
>> per site [cm]", xlim=c(20,3020), ylim=c(-2,5),  
>> col=coefficient2$color)
>> highlight(coefficient2$intercept ~ coefficient2$average_height,
>> lbls=coefficient2$site_no,col="Red", cex = .6)
>>
>> plot(coefficient2$intercept ~ coefficient2$average_dbh,
>> main="intercepts ::: dbh", ylab="intercepts", xlab="average dbh per
>> site [mm]", xlim=c(-10,360), ylim=c(-2,5),col=coefficient2$color )
>> highlight(coefficient2$intercept ~ coefficient2$average_dbh,
>> lbls=coefficient2$site_no,col="Red", cex = .6
>>
>>
>> If I create a temporary object for each plot excluding any NA values
>> for the x axis variable, somehow all points are displayed and the
>> labels are correct except for the color (I have e.g. no clue why some
>> points are red which I do not define at all and no ones are yellow
>> which I use several times).
>>
>> #create temp container for all coefficients with average heights for
>> plotting
>> coef_avheight <- coefficient2[which(! 
>> is.na(coefficient2$average_height)),]
>> plot(coef_avheight$intercept ~ coef_avheight$average_height,
>> main="intercepts ::: height", ylab="intercepts", xlab="average height
>> per site [cm]", xlim=c(20,3020), ylim=c(-2,5),
>> col=coef_avheight$color)
>> highlight(coef_avheight$intercept ~ coef_avheight$average_height,
>> lbls=coef_avheight$site_no,col="Red", cex = .6)
>>
>> #create temp container for all coefficients with average dbh for  
>> plotting
>> coef_avdbh<- coefficient2[which(!is.na(coefficient2$average_dbh)),]
>> plot(coef_avdbh$intercept ~ coef_avdbh$average_dbh,  main="intercepts
>> ::: dbh", ylab="intercepts", xlab="average dbh per site [mm]",
>> xlim=c(-10,360), ylim=c(-2,5),col=coef_avdbh$color )
>> highlight(coef_avdbh$intercept ~ coef_avdbh$average_dbh,
>> lbls=coef_avdbh$site_no,col="Red", cex = .6)
>>
>>
>> Maybe someone can explain me the color issue and the problem with the
>> NA values which results in a wrong labeling and to few
>> points being displayed? I'm new to R as you can guess and my code
>> isn't really elegant but I really cannot get faults within it...
>>
>>
>> Attached you can find the referred R object (coefficient2).
>> highlight requires library(NCStats)...
>>
>> Thank you very, very much,
>>
>>                       Katharina
>>
>> ______________________________________________
>> R-help at 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.
>>
>>
>
> -- 
> View this message in context: http://www.nabble.com/wrong-labels-and-colors-of-points-in-graph-plot-tp23873337p23873849.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at 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.

David Winsemius, MD
Heritage Laboratories
West Hartford, CT

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