I create a UK map representing some info by downloading an Spatial Polygons Data Frame from GADM.org and the following script.
lat<-c(51.5163,52.4847,51.4544,53.5933,51.481389,51.367778,55.953056,55.864167,51.482778)
lon<-c(-0.061389,-1.89,-2.587778,-2.296389,-3.178889,-0.07,-3.188056,-4.251667,-0.388056)
fr<-c(0.004278509,0.004111901,0.004150415,0.00421649,0.004221205,0.004191472,0.004507773,0.004314193,0.004098154)
uk<-data.frame(cbind(lat,lon,fr))
plotvar<-uk$fr
nclr<-4
plotclr <- brewer.pal(nclr,"Blues")
max.symbol.size=6
min.symbol.size=1
class <- classIntervals(plotvar, nclr, style="quantile")
colcode <- findColours(class, plotclr)
symbol.size <- ((plotvar-min(plotvar))/
(max(plotvar)-min(plotvar))*(max.symbol.size-min.symbol.size)
+min.symbol.size)
windows()
par(mai=c(0,0,0,0))
plot(UnK, col = 'lightgrey', border = 'darkgrey',xlim=c(-6,0),ylim=c(50,60)) #Unk is the map downloaded from GADM
points(uk$lon, uk$lat, col=2, pch=18)
points(uk$lon, uk$lat, pch=16, col=colcode, cex=symbol.size)
points(uk$lon, uk$lat, cex = symbol.size)
text(-120, 46.5, "Area: Frho")
legend(locator(1), legend=names(attr(colcode, "table")),
fill=attr(colcode, "palette"), cex=1, bty="n")
The following figure is the outcome of the above script.
Now, my problem is that I'm not happy with the colors and the breaks of the variable uk$fr. I need to change then in order to be able to compare this map with others, but I dont know how to do the following. My intention is to break this variable in 3 different classes like this (0-0.0125],(0.0125-0.0625],(0.0625-0.125]. And represent this classes by "Blues" and by different sizes circles. Also I want to force the legend to include these three classes.
One last question, how can I put title to the legend?
Thanks.
Related
I had created a raster stack when plotted looks like this:
I would like to change the titles on each of these graphs, and add a main title to it.
levelplot(rs, main = "MD13U0001", col.regions=rev(terrain.colors(6)), names.attr=c("LoCoH", "Elevation"))
When I try using the function levelplot it gives me this:
It puts both plots into the same scale, but gives me what I want in relation to the titles. Is there a better function that will give me the titles, but not keep the scales separate?
Example data
library(raster)
s <- stack(system.file("external/rlogo.grd", package="raster"))[[1:2]]
Set layer names and default plot
names(s) <- c("Apple", "Mango")
plot(s, cex.main=.8)
Some example customization
par(mar=c(3,3,5,5), mfrow=c(1,2))
for (i in 1:2) {
plot(s[[i]], cex.axis=.75, las=1)
title(names(s)[i], line=0.5, cex.main=0.8)
}
text(-40, 100, "These are my maps", xpd=NA, cex=2)
I´m recently trying to analyse my data and want to make the graphs a little nicer but I´m failing at this.
So I have a data set with 144 sites and 5 environmental variables. It´s basically about the substrate composition around an island and the fish abundance. On this island there is supposed to be a difference in the substrate composition between the north and the southside. Right now I am doing a pca and with the biplot function it works quite fine, but I would like to change the plot a bit.
I need one where the sites are just points and not numbered, arrows point to the different variable and the sites are colored according to their location (north or southside). So I tried everything i could find.
Most examples where with the dune data and suggested something like this:
library(vegan)
library(biplot)
data(dune)
mod <- rda(dune, scale = TRUE)
biplot(mod, scaling = 3, type = c("text", "points"))
So according to this I would just need to say text and points and R would label the variables and just make points for the sites. When i do this, however I get the Error:
Error in plot.default(x, type = "n", xlim = xlim, ylim = ylim, col = col[1L], :
formal argument "type" matched by multiple actual arguments
No idea how to get around this.
So next strategy I found, is to make a plot manually like this:
require("vegan")
data(dune, dune.env)
mod <- rda(dune, scale = TRUE)
scl <- 3 ## scaling == 3
colvec <- c("red2", "green4", "mediumblue")
plot(mod, type = "n", scaling = scl)
with(dune.env, points(mod, display = "sites", col = colvec[Use],
scaling = scl, pch = 21, bg = colvec[Use]))
text(mod,display="species", scaling = scl, cex = 0.8, col = "darkcyan")
with(dune.env, legend("bottomright", legend = levels(Use), bty = "n",
col = colvec, pch = 21, pt.bg = colvec))
This works fine so far as well, I get different colors and points, but now the arrows are missing. So I found that this should be corrected easy, if i just put "display="bp"" in the text line. But this doesn´t work either. Everytime I put "bp" R says:
Error in match.arg(display) :
argument "display" is missing, with no default
So I´m kind of desperate now. I looked through all the answers here and I don´t understand why display="bp" and type=c("text","points") is not working for me.
If anyone has an idea i would be super grateful.
https://www.dropbox.com/sh/y8xzq0bs6mus727/AADmasrXxUp6JTTHN5Gr9eufa?dl=0
This is the link to my dropbox folder. It contains my R-script and the csv files. The one named environmentalvariables_Kon1 also contains the data about north and southside.
So yeah...if anyone could help me. That would be awesome. I really don´t know what to do anymore.
Best regards,
Nancy
You can add arrows with arrows(). See the code for vegan:::biplot.rda to see how it works in the original function.
With your plot, add
g <- scores(mod, display = "species")
len <- 1
arrows(0, 0, len * g[, 1], len * g[, 2], length = 0.05, col = "darkcyan")
You might want to adjust the value of len to make the arrows longer
I am totally new to R.
I have expression profile data which is preprocessed and combined. Looks like this ("exp.txt")
STUDY_1_CANCER_1 STUDY_1_CON_1 STUDY_2_CANCER_1 STUDY_2_CANCER_2
P53 1.111 1.22 1.3 1.4
.....
Also, I created phenotype data. Looks lite this ("pheno.txt")
Sample Disease Study
STUDY_1_CANCER_1 Cancer GSE1
STUDY_1_CON_1 Normal GSE1
STUDY_2_CANCER_1 Cancer GSE2
STUDY_2_CON_1 Normal GSE2
Here, I tried to make MDS plot using classical cmdscale command like this.
data=read.table("exp.txt", row.names=1, header=T)
DATA=as.matrix(data)
pc=cor(DATA, method="p")
mds=cmdscale(as.dist(1-pc),2)
plot(mds)
I'd like to create plot like this figure with color double-labeling (Study and Disease). How should I do?
First create an empty plot, then add the points with specified colors/shapes.
Here's an example:
require(vegan)
data(dune)
data(dune.env)
mds <- cmdscale(vegdist(dune, method='bray'))
# set colors and shapes
cols = c('red', 'blue', 'black', 'steelblue')
shps = c(15, 16, 17)
# empty plot
plot(mds, type = 'n')
# add points
points(mds, col = cols[dune.env$Management], pch = shps[dune.env$Use])
# add legend
legend('topright', col=cols, legend=levels(dune.env$Management), pch = 16, cex = 0.7)
legend('bottomright', legend=levels(dune.env$Use), pch = shps, cex = 0.7)
Note that factors are internally coded as integers, which is helpful here.
> levels(dune.env$Management)
[1] "BF" "HF" "NM" "SF"
so
cols[dune.env$Management]
will take the first entry of cols for the first factor levels. Similariy for the different shapes.
Finally add the legend. Of course this plot still needs some polishing, but thats the way to go...
BTW: Gavin Simpson has a nice blogpost about customizing ordination plots.
Actually, you can do this directly in default plot command which can take pch and col arguments as vectors. Use:
with(data, plot(mds, col = as.numeric(Study), pch = as.numeric(Disease), asp = 1)
You must use asp = 1 when you plot cmdscale results: both axes must be scaled similarly. You can also add xlab and ylab arguments for nicer axis labels. For adding legend and selecting plotting characters and colours, see other responses.
I am an absolute beginner in R. so this is probably a stupid question.
I have a table like this (csv format):
,1A+,2A+,3A-,3A+,5A-,5A+,6A-,6A+,7A-,7A+
6,4.530309305,5.520356001,3.437626731,5.146758132,,4.355022819,,4.191337618,,4.076583859
10,8.697814022,9.765817956,,9.636004092,3.725756716,8.600484774,3.457423715,8.358842335,2.246622784,7.244668991
12,,,8.176341701,,,,,,,
17,,,,,6.24785396,,5.077069513,,3.137524578
I want to create a line graph in R plotting all the different Y values (1A+, 2A+, etc) vs the Y values (6,10,12,17).
I am doing:
new_curves <- read.csv("new_curves_R.csv", as.is = TRUE)
g_range <- range(0,new_curves$X)
axis(2, las=1, at=4*0:g_range[2])
plot(new_curves$X1A.,new_curves$X,type="o", col="blue")
legend(1, g_range[2], c("new_curves$X1A."), cex=0.8, col=c("blue"));
title(xlab="Days", col.lab=rgb(0,0.5,0))
title(ylab="Total", col.lab=rgb(0,0.5,0))
However, this (obviously) only plots the first datapoint. (the legend is not working for some reason either). I am guessing I need some sort of for loop to add each Y value to the graph recursively. Likewise, a loop would be needed to make the legend.
thanks
dat <- read.table(text=", 1A+,2A+,3A-,3A+,5A-,5A+,6A-,6A+,7A-,7A+
6,4.530309305,5.520356001,3.437626731,5.146758132,,4.355022819,,4.191337618,,4.076583859
10,8.697814022,9.765817956,,9.636004092,3.725756716,8.600484774,3.457423715,8.358842335,2.246622784,7.244668991
12,,,8.176341701,,,,,,,
17,,,,,6.24785396,,5.077069513,,3.137524578", header=TRUE, sep=",", fill=TRUE)
matplot(dat[1], dat[-1])
I have a plot which plots points with a particular symbol and color. I want my legend to show the exact same colors and symbols as those in the plot. I can do this manually, but I have over 50 plots to generate and data is going to be conually updated so I would like to automate the process. I tried to create a dictionary and wanted to search the dictionary. If the value was found in levels(Color_test), then color the symbol in legend the same as outlined in the dictionary.
My legend code is as follows:
legend(legend_X, legend_Y,
xjust=x_adj, yjust=y_adj,
levels(Color_test),
col=Labels.col,
pch=Labels.sym,
horiz=FALSE)
May be what you are looking for is some kind of merging your data with the dictionary. Here is how it is done with only colors as it is just an example
data <- data.frame(type = sample(letters[1:3],20,replace=T),
x = runif(20),
y = runif(20))
dict <- data.frame(type = letters[1:4],
color = c("red","green","blue","black"))
plot(data$x, data$y, col = merge(data,dict)$color)
legend("topleft",legend=dict$type, col=dict$color, pch=1)
Easily you can modify the legend so that is justs displays the actually used colors.
data_dict <- merge(data,dict)
plot(y~x, col=color, data=data_dict, pch=as.vector(type))
legend("topleft",legend=unique(data_dict$type), col=unique(data_dict$color), pch=1)