Thanks Bill and David
Here goes an example
SP1<-c(9,6,7,8,5,8,7,5,9,7)
SP2<-c(1,3,4,2,4,2,5,3,2,1)
SP3<-c(4,6,7,5,7,8,7,6,5,4)
SP4<-c(5,4,3,5,2,3,4,3,4,2)
mydata<-data.frame(SP1,SP2,SP3,SP4)
rownames(mydata)<-c("ST1","ST2","ST3","ST4","ST5","ST6","ST7","ST8","ST9","ST10")
mydata
boxplot(mydata)
Note that this data frame does not have the format Response ~ Group. In my
real matrix I have up to 40 species.
Is there any way to have the species ordered by their median abundance (or
other parameter?)
The desired order is given by names(sort(apply(mydata,2,median)))
Thanks once more,
Antonio Olinto
Fisheries Institute
Sao Paulo, Brazil
2015-03-21 15:13 GMT-03:00 William Dunlap <wdunlap at tibco.com>:
> You can use the reorder() function to reorder the grouping vector's
> factor levels according to a function of the data in each group. E.g.,
> compare the following two plots:
>
> d <- data.frame(Response=cos(1:15),
Group=rep(c("A","B","C"),c(6,5,4)))
> par(mfrow=c(1,2))
> boxplot(Response ~ Group, data=d)
> boxplot(Response ~ reorder(Group, X=Response, FUN=median), data=d)
>
>
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com
>
> On Fri, Mar 20, 2015 at 2:20 PM, Antonio Silva <aolinto.lst at
gmail.com>
> wrote:
>
>> Hello
>>
>> I'm using a dataframe (mydata) where row names are sampling points
and
>> column names are species in a multivariate analysis.
>>
>> If I write boxplot(mydata) I'll have boxplots for each species
abundance
>> in
>> alphabetical order.
>>
>> How to get the boxes orderer by the median?
>>
>> Usually for this I write
>>
>>
boxplot(value~category,at=rank(tapply(mydata$value,mydata$category,median)))
>> but for this to work I need a column for the categories and another
column
>> for the values.
>>
>> Thanks in advance, best regards.
>>
>> Antonio Olinto
>>
>> [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> 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.
>>
>
>
[[alternative HTML version deleted]]
There may be more concise ways to do this - but you are 99% there with your approach: try: boxplot(mydata[,names(sort(apply(mydata,2,median)))]) B. On Mar 21, 2015, at 6:49 PM, Antonio Silva <aolinto.lst at gmail.com> wrote:> Thanks Bill and David > > Here goes an example > > SP1<-c(9,6,7,8,5,8,7,5,9,7) > SP2<-c(1,3,4,2,4,2,5,3,2,1) > SP3<-c(4,6,7,5,7,8,7,6,5,4) > SP4<-c(5,4,3,5,2,3,4,3,4,2) > mydata<-data.frame(SP1,SP2,SP3,SP4) > rownames(mydata)<-c("ST1","ST2","ST3","ST4","ST5","ST6","ST7","ST8","ST9","ST10") > mydata > boxplot(mydata) > > Note that this data frame does not have the format Response ~ Group. In my > real matrix I have up to 40 species. > > Is there any way to have the species ordered by their median abundance (or > other parameter?) > > The desired order is given by names(sort(apply(mydata,2,median))) > > Thanks once more, > > Antonio Olinto > Fisheries Institute > Sao Paulo, Brazil > > 2015-03-21 15:13 GMT-03:00 William Dunlap <wdunlap at tibco.com>: > >> You can use the reorder() function to reorder the grouping vector's >> factor levels according to a function of the data in each group. E.g., >> compare the following two plots: >> >> d <- data.frame(Response=cos(1:15), Group=rep(c("A","B","C"),c(6,5,4))) >> par(mfrow=c(1,2)) >> boxplot(Response ~ Group, data=d) >> boxplot(Response ~ reorder(Group, X=Response, FUN=median), data=d) >> >> >> Bill Dunlap >> TIBCO Software >> wdunlap tibco.com >> >> On Fri, Mar 20, 2015 at 2:20 PM, Antonio Silva <aolinto.lst at gmail.com> >> wrote: >> >>> Hello >>> >>> I'm using a dataframe (mydata) where row names are sampling points and >>> column names are species in a multivariate analysis. >>> >>> If I write boxplot(mydata) I'll have boxplots for each species abundance >>> in >>> alphabetical order. >>> >>> How to get the boxes orderer by the median? >>> >>> Usually for this I write >>> >>> boxplot(value~category,at=rank(tapply(mydata$value,mydata$category,median))) >>> but for this to work I need a column for the categories and another column >>> for the values. >>> >>> Thanks in advance, best regards. >>> >>> Antonio Olinto >>> >>> [[alternative HTML version deleted]] >>> >>> ______________________________________________ >>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >>> 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. >>> >> >> > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > 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.
... just for completeness - the more concise way: (no need to go through names()). boxplot(mydata[,order(apply(mydata,2,median))]) ... or descending boxplot(mydata[,order(-apply(mydata,2,median))]) B. On Mar 21, 2015, at 7:04 PM, Boris Steipe <boris.steipe at utoronto.ca> wrote:> There may be more concise ways to do this - but you are 99% there with your approach: > try: > > boxplot(mydata[,names(sort(apply(mydata,2,median)))]) > > B. > > > On Mar 21, 2015, at 6:49 PM, Antonio Silva <aolinto.lst at gmail.com> wrote: > >> Thanks Bill and David >> >> Here goes an example >> >> SP1<-c(9,6,7,8,5,8,7,5,9,7) >> SP2<-c(1,3,4,2,4,2,5,3,2,1) >> SP3<-c(4,6,7,5,7,8,7,6,5,4) >> SP4<-c(5,4,3,5,2,3,4,3,4,2) >> mydata<-data.frame(SP1,SP2,SP3,SP4) >> rownames(mydata)<-c("ST1","ST2","ST3","ST4","ST5","ST6","ST7","ST8","ST9","ST10") >> mydata >> boxplot(mydata) >> >> Note that this data frame does not have the format Response ~ Group. In my >> real matrix I have up to 40 species. >> >> Is there any way to have the species ordered by their median abundance (or >> other parameter?) >> >> The desired order is given by names(sort(apply(mydata,2,median))) >> >> Thanks once more, >> >> Antonio Olinto >> Fisheries Institute >> Sao Paulo, Brazil >> >> 2015-03-21 15:13 GMT-03:00 William Dunlap <wdunlap at tibco.com>: >> >>> You can use the reorder() function to reorder the grouping vector's >>> factor levels according to a function of the data in each group. E.g., >>> compare the following two plots: >>> >>> d <- data.frame(Response=cos(1:15), Group=rep(c("A","B","C"),c(6,5,4))) >>> par(mfrow=c(1,2)) >>> boxplot(Response ~ Group, data=d) >>> boxplot(Response ~ reorder(Group, X=Response, FUN=median), data=d) >>> >>> >>> Bill Dunlap >>> TIBCO Software >>> wdunlap tibco.com >>> >>> On Fri, Mar 20, 2015 at 2:20 PM, Antonio Silva <aolinto.lst at gmail.com> >>> wrote: >>> >>>> Hello >>>> >>>> I'm using a dataframe (mydata) where row names are sampling points and >>>> column names are species in a multivariate analysis. >>>> >>>> If I write boxplot(mydata) I'll have boxplots for each species abundance >>>> in >>>> alphabetical order. >>>> >>>> How to get the boxes orderer by the median? >>>> >>>> Usually for this I write >>>> >>>> boxplot(value~category,at=rank(tapply(mydata$value,mydata$category,median))) >>>> but for this to work I need a column for the categories and another column >>>> for the values. >>>> >>>> Thanks in advance, best regards. >>>> >>>> Antonio Olinto >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> ______________________________________________ >>>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >>>> 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. >>>> >>> >>> >> >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >> 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. > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > 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.