Re: [R-sig-phylo] ape package: improvement suggestion in color handling for mosaic in phydataplot?
Elizabeth,
Thanks a lot for the detailed account of this problem. I've just made
these modifications to the code of phydataplot:
1/ Replaced:
lgd <- as.character(ux)
with:
lgd <- sort(as.character(ux))
2/ These two lines:
conames <- names(co)
if (!is.null(conames)) co <- co[lgd]
were inserted after:
co <- funcol(nux)
These seem to produce the effects you requested. Particularly, using
either f or fb as argument to funcol produces the same output:
f <- function(n) c("yellow", "blue", "red")
fb <- function(n) c("3" = "red", "2" = "blue", "1" = "yellow")
I'll soon upload a patch to ape's site (will be version 4.1-0.4). A
Windows version will follow soon.
Cheers,
Emmanuel
Le 24/05/2017 à 06:17, Elizabeth Purdom a écrit :
Dear all,
I am trying to use the phydataplot function in the ape package with the
style mosaic. I am having difficulty getting the colors of the
rectangles to be the color I desire in an automatic way. I have come to
the conclusion that I can’t do and it would have to be an enhancement to
the package, though I would be glad to know I am wrong.
Here is the example in phydataplot for how to set the colors
set.seed(1378923)
## use type = "mosaic" on a 30x5 matrix:
tr <- rtree(n <- 30)
p <- 5
x <- matrix(sample(3, size = n*p, replace = TRUE), n, p)
dimnames(x) <- list(paste0("t", 1:n), LETTERS[1:p])
plot(tr, x.lim = 35, align.tip = TRUE, adj = 1)
phydataplot(x, tr, "m", 2, width = 2, border = "white", lwd = 3, legend
= "side")
f <- function(n) c("yellow", "blue", "red")
phydataplot(x, tr, "m", 18, width = 2, border = "white", lwd = 3,
legend = "side", funcol = f)
Notice we set the colors with the function c("yellow", "blue", "red”).
However, we see when we plot them, that this assignment resulted in
2=yellow, 3=blue, 1=red. If instead I want 1=yellow, 2=blue, 3=red, I
can use this plot I just made to see how they should be ordered to get
my desired color assignment, and rearrange the colors:
plot(tr, x.lim = 35, align.tip = TRUE, adj = 1)
phydataplot(x, tr, "m", 2, width = 2, border = "white", lwd = 3, legend
= "side")
f <- function(n) c("blue", "red", "yellow")
phydataplot(x, tr, "m", 18, width = 2, border = "white", lwd = 3,
legend = "side", funcol = f)
However, I see no way to do this without first plotting them, manually
looking at the arbitrary order created, and then fixing it.Yet, I would
like to do this in an automatic fashion — I’m trying to build a function
on top of this function — so I need to know ahead of time how
phydataplot will assign the colors (and so if my tree changes it will
still give the desired colors).Looking at the internal function, the
relevant stream of code is the following (i.e. cutting away the parts
not needed for determining the colors) and shows that the assignment of
colors to data is entirely dependent on the order of the data after the
function internally matches it to the tree:
lastPP <- get("last_plot.phylo", envir = .PlotPhyloEnv)
x <- .matchDataPhylo(x, phy)
n <- length(phy$tip.label)
one2n <- seq_len(n)
lastPP <- get("last_plot.phylo", envir = .PlotPhyloEnv)
y1 <- lastPP$yy[one2n]
o <- order(y1)
x <- if (style == "image") x[o, o]
else if (is.vector(x)) x[o]
else x[o, ]
nux <- length(ux <- unique.default(x))
x <- match(x, ux)
co <- funcol(nux)
rect(xl, yb, xr, yt, col = co[x], xpd = TRUE, ...)
This means that the colors provide by the user are assigned to the
values of unique(x) *after* x is reordered internally by .matchDataPhylo
and then again reordered x[o,], where o is the order of the tips of the
tree in the plot, I believe. This is not something returned to the user,
unfortunately, by plot.phylo, but is assigned to an hidden environment
variable :
assign("last_plot.phylo", c(L, list(edge = xe, xx = xx, yy = yy)),
envir = .PlotPhyloEnv)
These seems to make it next to impossible to get the right colors
without just trying it out interactively. If anyone had any other
alternatives I’d love to hear them.
I’ve tried making a little function:
getColFun<-function(x,phy,namedColors){
x <- ape:::.matchDataPhylo(x, phy)
n <- length(phy$tip.label)
one2n <- seq_len(n)
lastPP <- get("last_plot.phylo", envir = .PlotPhyloEnv)
y1 <- lastPP$yy[one2n]
o <- order(y1)
ux<-unique.default(x[o])
m<-match(as.character(ux),names(namedColors))
function(n){namedColors[m]}
}
But it’s a bit awkward because it relies on .PlotPhyloEnv which is not
always available if you haven’t loaded the package, as well as the
internal function .matchDataPhylo. This is problematic for putting it
into a package. Is there a function I’m not aware of that would be helpful?
In terms of enhancement, it would be nice if instead phydataplot
accepted a named vector of colors, where the vector of colors is
required to have names that match the values of the data in x, and then
the phydataplot internally would figure out how to match them together.
Less desirable would
[R-sig-phylo] ape package: improvement suggestion in color handling for mosaic in phydataplot?
Dear all,
I am trying to use the phydataplot function in the ape package with the style
mosaic. I am having difficulty getting the colors of the rectangles to be the
color I desire in an automatic way. I have come to the conclusion that I can’t
do and it would have to be an enhancement to the package, though I would be
glad to know I am wrong.
Here is the example in phydataplot for how to set the colors
set.seed(1378923)
## use type = "mosaic" on a 30x5 matrix:
tr <- rtree(n <- 30)
p <- 5
x <- matrix(sample(3, size = n*p, replace = TRUE), n, p)
dimnames(x) <- list(paste0("t", 1:n), LETTERS[1:p])
plot(tr, x.lim = 35, align.tip = TRUE, adj = 1)
phydataplot(x, tr, "m", 2, width = 2, border = "white", lwd = 3, legend =
"side")
f <- function(n) c("yellow", "blue", "red")
phydataplot(x, tr, "m", 18, width = 2, border = "white", lwd = 3,
legend = "side", funcol = f)
Notice we set the colors with the function c("yellow", "blue", "red”).
However, we see when we plot them, that this assignment resulted in 2=yellow,
3=blue, 1=red. If instead I want 1=yellow, 2=blue, 3=red, I can use this plot I
just made to see how they should be ordered to get my desired color assignment,
and rearrange the colors:
plot(tr, x.lim = 35, align.tip = TRUE, adj = 1)
phydataplot(x, tr, "m", 2, width = 2, border = "white", lwd = 3, legend =
"side")
f <- function(n) c("blue", "red", "yellow")
phydataplot(x, tr, "m", 18, width = 2, border = "white", lwd = 3,
legend = "side", funcol = f)
However, I see no way to do this without first plotting them, manually looking
at the arbitrary order created, and then fixing it. Yet, I would like to do
this in an automatic fashion — I’m trying to build a function on top of this
function — so I need to know ahead of time how phydataplot will assign the
colors (and so if my tree changes it will still give the desired colors).
Looking at the internal function, the relevant stream of code is the following
(i.e. cutting away the parts not needed for determining the colors) and shows
that the assignment of colors to data is entirely dependent on the order of the
data after the function internally matches it to the tree:
lastPP <- get("last_plot.phylo", envir = .PlotPhyloEnv)
x <- .matchDataPhylo(x, phy)
n <- length(phy$tip.label)
one2n <- seq_len(n)
lastPP <- get("last_plot.phylo", envir = .PlotPhyloEnv)
y1 <- lastPP$yy[one2n]
o <- order(y1)
x <- if (style == "image") x[o, o]
else if (is.vector(x)) x[o]
else x[o, ]
nux <- length(ux <- unique.default(x))
x <- match(x, ux)
co <- funcol(nux)
rect(xl, yb, xr, yt, col = co[x], xpd = TRUE, ...)
This means that the colors provide by the user are assigned to the values of
unique(x) *after* x is reordered internally by .matchDataPhylo and then again
reordered x[o,], where o is the order of the tips of the tree in the plot, I
believe. This is not something returned to the user, unfortunately, by
plot.phylo, but is assigned to an hidden environment variable :
assign("last_plot.phylo", c(L, list(edge = xe, xx = xx, yy = yy)),
envir = .PlotPhyloEnv)
These seems to make it next to impossible to get the right colors without just
trying it out interactively. If anyone had any other alternatives I’d love to
hear them.
I’ve tried making a little function:
getColFun<-function(x,phy,namedColors){
x <- ape:::.matchDataPhylo(x, phy)
n <- length(phy$tip.label)
one2n <- seq_len(n)
lastPP <- get("last_plot.phylo", envir = .PlotPhyloEnv)
y1 <- lastPP$yy[one2n]
o <- order(y1)
ux<-unique.default(x[o])
m<-match(as.character(ux),names(namedColors))
function(n){namedColors[m]}
}
But it’s a bit awkward because it relies on .PlotPhyloEnv which is not always
available if you haven’t loaded the package, as well as the internal function
.matchDataPhylo. This is problematic for putting it into a package. Is there a
function I’m not aware of that would be helpful?
In terms of enhancement, it would be nice if instead phydataplot accepted a
named vector of colors, where the vector of colors is required to have names
that match the values of the data in x, and then the phydataplot internally
would figure out how to match them together. Less desirable would be if the
output of plot.phylo returned the information in ‘L’ that is saved in the
.PlotPhyloEnv, then I could at least recreate a more stable version of my
little function above.
(it would also be nice if the legend of the colors was in some reasonable
sorted order, i.e. 1,2,3, and not in the arbitrary order)
Thanks,
Elizabeth Purdom
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