[R] How to find out if two cells in a dataframe belong to the same pre-specified factor-level
Tim Richter-Heitmann
trichter at uni-bremen.de
Tue Sep 29 11:27:33 CEST 2015
Thank you, that turned out to work very well.
If you want to, you can answer it here:
http://stackoverflow.com/questions/32809249/how-to-find-out-if-two-cells-in-a-dataframe-belong-to-the-same-pre-specified-fac/
The question wasnt properly answered, which is why i switched to R-list.
On 28.09.2015 20:15, Adams, Jean wrote:
> Here's one approach that works. I made some changes to the code you
> provided. Full working example code given below.
>
> library(reshape)
> library(ggplot2)
> library(dplyr)
>
> dist1 <- matrix(runif(16), 4, 4)
> dist2 <- matrix(runif(16), 4, 4)
> rownames(dist1) <- colnames(dist1) <- paste0("A", 1:4)
> rownames(dist2) <- colnames(dist2) <- paste0("A", 1:4)
> m1 <- melt(dist1)
> m2 <- melt(dist2)
> # I changed the by= argument here
> final <- full_join(m1, m2, by=c("X1", "X2"))
>
> # I made some changes to keep spcs character and grps factor
> species <- data.frame(spcs=paste0("A", 1:4),
> grps=as.factor(c(rep("cat", 2), (rep("dog", 2)))),
> stringsAsFactors=FALSE)
>
> # define new variables for final indicating group membership
> final$g1 <- species$grps[match(final$X1, species$spcs)]
> final$g2 <- species$grps[match(final$X2, species$spcs)]
> final$group <- as.factor(with(final, ifelse(g1==g2, as.character(g1),
> "dif")))
>
> # plot just the rows with matching groups
> ggplot(final[final$group!="dif", ], aes(value.x, value.y, col=group)) +
> geom_point()
> # plot all the rows
> ggplot(final, aes(value.x, value.y, col=group)) + geom_point()
>
> Jean
>
>
> On Sun, Sep 27, 2015 at 4:22 PM, <trichter at uni-bremen.de
> <mailto:trichter at uni-bremen.de>> wrote:
>
> Dear list,
> I really couldnt find a better way to describe my question, so
> please bear with me.
>
> To illustrate my problem, i have a matrix with ecological
> distances (m1) and one with genetic distances (m2) for a number of
> biological species. I have merged both matrices and want to plot
> both distances versus each other, as illustrated in this example:
>
> library(reshape)
> library(ggplot2)
> library(dplyr)
>
> dist1 <- matrix(runif(16),4,4)
> dist2 <- matrix(runif(16),4,4)
> rownames(dist1) <- colnames(dist1) <- paste0("A",1:4)
> rownames(dist2) <- colnames(dist2) <- paste0("A",1:4)
>
> m1 <- melt(dist1)
> m2 <- melt(dist2)
>
> final <- full_join(m1,m2, by=c("Var1","Var2"))
> ggplot(final, aes(value.x,value.y)) + geom_point()
>
> Here is the twist:
> The biological species belong to certain groups, which are given
> in the dataframe `species`, for example:
>
> species <- data.frame(spcs=as.character(paste0("A",1:4)),
> grps=as.factor(c(rep("cat",2),(rep("dog",2)))))
>
> I want to check if a x,y pair in final (as in `final$Var1`,
> `final$Var2`) belongs to the same group of species (here "cat" or
> "dog"), and then want to color all groups specifically in the
> x,y-scatterplot.
> Thus, i need an R translation for:
>
> final$group <- If (final$Var1 and final$Var2) belong to the same
> group as specified
> in species, then assign the species group here, else do
> nothing or assign NA
>
> so i can proceed with
>
> ggplot(final, aes(value.x,value.y, col=group)) + geom_point()
>
> So, in the example, the pairs A1-A1, A1-A2, A2-A1, A2-A2 should be
> identified as "both cats", hence should get the factor "cat".
>
> Thank you very much!
>
>
> Tim
>
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--
Tim Richter-Heitmann (M.Sc.)
PhD Candidate
International Max-Planck Research School for Marine Microbiology
University of Bremen
Microbial Ecophysiology Group (AG Friedrich)
FB02 - Biologie/Chemie
Leobener Straße (NW2 A2130)
D-28359 Bremen
Tel.: 0049(0)421 218-63062
Fax: 0049(0)421 218-63069
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