I am trying to add the species names to the rankabuncomp plot. I tried to add specnames = T to the rankabundance function but I get an error. Please help me work around this problem. Thanks a lot.
library(vegan)
library(BiodiversityR)
data(dune.env)
data(dune)
RankAbun.1 <- rankabundance(dune)
RankAbun.1
rankabunplot(RankAbun.1,scale='abundance', addit=FALSE, specnames=c(1,2,3))
rankabuncomp(dune, y=dune.env, factor='Management', scale='proportion', legend=FALSE)
#to add specnames
rankabuncomp(dune, y=dune.env, factor='Management', specnames=c(1,2,3), scale='proportion', legend=FALSE, labels=FALSE)
BiodiversityR::rankabuncomp explicitly disallows adding species names. This is hardcoded in the function and cannot be changed without editing the function (look for specnames = NULL in rankabunplot() calls). The help page does not give specnames argument to rankabuncomp so that this is also documented. I can understand this decision: rankabuncomp draws several lines in one graph, and often these are so similar that species names would overwrite each other and the plot becomes unreadable.
To add the lines, you either need edit the function or you must use a series of rankabunplot commands to overlay graphs in one plot. Here is an example how to do that with the dune data:
library(BiodiversityR)
data(dune, dune.env)
## list of models
mods <- with(dune.env, lapply(levels(Management), function(lev)
rankabundance(dune, dune.env, 'Management', lev)))
## level 4 seems to be most extreme: draw it first
rankabunplot(mods[[4]],scale='abundance', addit=FALSE, specnames=c(1,2,3))
## add the rest
## change colour etc to separate the lines if wished
rankabunplot(mods[[3]],scale='abundance', addit=TRUE, specnames=c(1,2,3))
rankabunplot(mods[[2]],scale='abundance', addit=TRUE, specnames=c(1,2,3))
rankabunplot(mods[[1]],scale='abundance', addit=TRUE, specnames=c(1,2,3))
The resulting plot is not very readable. If you use proportional scaling of y-axis, it becomes even less readable. However, you can do it.
Related
This is the function that is part of FactorMiner package
https://github.com/cran/FactoMineR/blob/master/R/plot.HCPC.R
As an example this is the code I ran
res.pca <- PCA(iris[, -5], scale = TRUE)
hc <- HCPC(res.pca, nb.clust=-1,)
plot.HCPC(hc, choice="3D.map", angle=60)
hc$call$X$clust <- factor(hc$call$X$clust, levels = unique(hc$call$X$clust))
plot(hc, choice="map")
The difference is when i run this hc$call$X$clust <- factor(hc$call$X$clust, levels = unique(hc$call$X$clust))
before plot.HCPC this doesn't change the annotation in the figure but when I do the same thing before I ran this plot(hc, choice="map") it is reflected in the final output.
When i see the plot.HCPC function this is the line of the code that does embed the cluster info into the figure
for(i in 1:nb.clust) leg=c(leg, paste("cluster",levs[i]," ", sep=" "))
legend("topleft", leg, text.col=as.numeric(levels(X$clust)),cex=0.8)
My question I have worked with small function where I understand when i edit or modify which one goes where and does what here in this case its a complicated function at least to me so Im not sure how do I modify that part and get what I would like to see.
I would like to see in case of my 3D dendrogram each of the cluster are labelled with group the way we can do in complexheatmap where we can annotate that are in row or column with a color code so it wont matter what the order in the data-frame we can still identify(it's just visual thing I know but I would like to learn how to modify these)
I am plotting maps of atmospheric pollutant fields, or meteorological field, difference between such fields, often overlayed with orography.
My fields are gridded.
A white line misteriously appears, sometimes two.
This seems to happen a bit randomly. I mean: same code and fields, same line; but when I change fields, or color scales, it changes position, or it disappears, or another one appears. Sometimes horizontal, sometimes vertical.
Here is my code
#!/usr/bin/env Rscript
library(rasterVis)
library(RColorBrewer)
NX <- 468
NY <- 421
hgt <- matrix(0.,NX,NY)
# read from file:
ucon <- file("hgt.dat", open="rb")
for (n in seq(1,NX)) {
hgt[n,] <- readBin(ucon, "numeric", n=NY, size=4)
}
close(ucon)
hgtbks <- c(-100,10,500,1000,1500,2000,2500,3000,3500)
hgtcols <- colorRampPalette(c("gray30","white"))(length(hgtbks)-1)
tit <- "Orography"
bkstart=50.0; bkmax=1500.; bkby=100.
bks <- seq(bkstart, bkmax, bkby)
nbks <- length(bks)
cols <- rev(colorRampPalette(brewer.pal(11,"Spectral"))(nbks-2))
cols <- c("white",cols)
legendbreaks <- seq(1,nbks)
legendlabels <- formatC(bks,digits=3)
legendlabpos <- legendbreaks
rpl <-
levelplot(hgt, margin=FALSE , col.regions= hgtcols, at= hgtbks
, main= list(label=tit, cex=1.8)
, colorkey=list(draw= TRUE, col=cols, at=legendbreaks
, labels=list(labels=legendlabels, at=legendlabpos, cex=1.2))
, xlab=NULL, ylab=NULL, scales= list(draw= FALSE))
png("whiteline.png", width=800, height=840)
plot(rpl)
graphics.off()
I would really like to upload a file with my data, but for the moment
I could not find a way to do it (I don't think I can do it, not even an ASCII file). The data matrix (468x421) is too big to be explicitly included in the code, but it really is the orography file
shown in the picture (elevation in meters above mean sea level).
And here is the resulting "white line" map:
Really, I think this might be a levelplot bug. It seems to happen both when hgt is a matrix and when it is a proper raster object: this doesn't seem to make a difference.
Any idea?
I think I found a workaround.
By setting zero padding on the 4 sides, I managed to make the whiteline disappear from a series of maps.
First I defined:
zpadding <- list(layout.heights= list(top.padding=0, bottom.padding=0),
layout.widths= list(left.padding=0, right.padding=0))
then I added, among the parameters of the levelplot call:
par.settings=zpadding
As I said, I don't think this is a proper solution, but a workaround.
The problem seems related to any rescaling of the plot area.
In fact, when a rescaling is forced by, for example, having 4 or 5 digits (instead of 2 or 3) in the colorbar labels, a white line may reappear.
I hope this may point in the right direction other people, either users or developers of levelplot and related software.
I am attempting to produce an NMDS plot in vegan, but really struggling with the code. I am trying to display the site points and species points differently, with the site points coloured according to treatment. Both lines work individually, but I cannot work out how to combine these two lines of code into one line to form one graph. I am using ordipointlabel to prevent overlap. These are the two lines of code I want to combine into one.
ordipointlabel(NMDS10, scaling=2, display="species", select=sel)
ordipointlabel(NMDS10,display="sites", col=c(rep("darkgreen",4),rep("blue4",4)),cex=0.75)
You can access directly to ordinpointlabel object and make it look like you wish. Please see the sample:
library(vegan)
data(dune)
NMDS10 <- metaMDS(dune[1:8, ])
pdf(file = NULL)
y <- ordipointlabel(NMDS10, display=c("sites", "species"))
dev.off()
# select sites & species
sel <- unlist(dimnames(dune[1:8, ]))[-(20:ncol(dune))]
# messing with ordipointlabel object
y$points <- y$points[rownames(y$points) %in% sel, ]
y$args$pcol[] = rep("red", length(y$args$pcol))
y$args$pcol[1:8] <- c(rep("darkgreen", 4), rep("blue4", 4))
y$par$cex <- 0.75
plot(y)
I was experimenting with the waffle package in r, and was trying to use a for loop to make multiple plots at once but was not able to get my code to work. I have a dataset with values for each year of renewables,and since it is over 40 years of data, was looking for a simple way to plot these with a for loop rather than manyally year by year. What am I doing wrong?
I have it from 1:16 as an experiment to see if it would work, although in reality I would do it for all the years in my dataset.
for(i in 1:16){
renperc<-islren$Value[i]
parts <- c(`Renewable`=(renperc), `Non-Renewable`=100-renperc)
waffle(parts, rows=10, size=1, colors=c("#00CC00", "#A9A9A9"),
title="Iceland Primary Energy Supply",
xlab=islren$TIME)
}
If I get your question correctly you want to plot all the 16 iterations in a same panel? You can parametrise your plot window to be divided into 16 smaller plots using par(mfrow = c(4,4)) (creating a 4 by 4 matrix and plotting into each cells recursively).
## Setting the graphical parameters
par(mfrow = c(4,4))
## Running the loop normally
for(i in 1:16){
renperc<-islren$Value[i]
parts <- c(`Renewable`=(renperc), `Non-Renewable`=100-renperc)
waffle(parts, rows=10, size=1, colors=c("#00CC00", "#A9A9A9"),
title="Iceland Primary Energy Supply",
xlab=islren$TIME)
}
If you need more plots (e.g. 40) you can increase the numbers in the graphical parameters (e.g. par(mfrow = c(6,7))) but that will create really tiny plots. One solution is to do it in multiple loops (for(i in 1:16); for(i in 17:32); etc.)
UPDATE: The code simply wasn't plotting anything when i tried putting in anything above one value (ex. 1:16) or a letter, both in terms of separate plots or many in one plot window (which I think perhaps waffle does not support in the same way as regular plots). In the end, I managed by making it into a function, although I'm still not sure why my original method wouldn't work if this did. See the code that worked below. I also tweaked it a bit, adding ggsave for example.
#function
waffling <- function(x){
renperc<-islren$Value[x]
parts <- c(`Renewable`=(renperc), `Non-Renewable`=100-renperc)
waffle(parts, rows=10, size=1, colors=c("#00CC00", "#A9A9A9"), title="",
xlab=islren$TIME[x])
ggsave(file=paste0("plot_", x,".png"))}
for(i in 1:57){
waffling(i)
}
I am trying to use the animation package to generate an "evolving" plot of points on a map. The map is generated from shapefiles (from the readShapeSpatial/readShapeLines functions).
The problem is when it's plotted in a for loop, the result is additive, whereas the ideal result is to have it evolve.
Are there ways of using par() that I am missing?
My question is: is there a way to clear just the points ploted from the points function
and not clearing the entire figure thus not having to regraph the shapefiles?
in case someone wants to see code:
# plotting underlying map
newyork <- readShapeSpatial('nycpolygon.shp')
routes <- readShapeLines('nyc.shp')
par(bg="grey25")
plot(newyork, lwd=2, col ="lightgray")
plot(routes,add=TRUE,lwd=0.1,col="lightslategrey")
# plotting points and save to GIF
ani.options(interval=.05)
saveGIF({
par(bg="grey25")
# Begin loop
for (i in 13:44){
infile <-paste("Week",i,".csv",sep='')
mydata <-read.csv(file = infile, header = TRUE, sep=",")
plotvar <- Var$Para
nclr <- 4
plotclr <-brewer.pal(nclr,"RdPu")
class<- classIntervals(plotvar,nclr,style = "pretty")
colcode <- findColours(class,plotclr)
points(Var$Lon,Var$Lat,col=colcode)
}
})
If you can accept a residual shadow or halo of ink, you can over-plot with color ="white" or == to your background choices. We cannot access your shape file but you can try it out by adding this line:
points(Var$Lon, Var$Lat, col="grey25")
It may leave gaps in other previously plotted figures or boundaries, because it's definitely not object-oriented. The lattice and ggplot2 graphics models are more object oriented, so if you want to post a reproducible example, that might be an alternate path to "moving" forward. I seem to remember that the rgl package has animation options in its repetoire.