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])
Related
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.
Hopefully a straightforward question but I made a simple figure in R using filled.contour(). It looks fine, and what it should like given the data. However, I want to add a reference line along a contour for 0 (level = 0), and the plotted line doesn't match the colors on the filled.contour figure. The line is close, but not matching with the figure (and eventually crossing over another contour from the filled.contour plot). Any ideas why this is happening?
aa <- c(0.05843150, 0.11300040, 0.15280030, 0.183524400, 0.20772430, 0.228121000)
bb <- c(0.01561055, 0.06520635, 0.10196237, 0.130127650, 0.15314544, 0.172292410)
cc <- c(-0.02166599, 0.02306650, 0.05619421, 0.082193680, 0.10334837, 0.121156780)
dd <- c(-0.05356592, -0.01432910, 0.01546647, 0.039156660, 0.05858709, 0.074953650)
ee <- c(-0.08071987, -0.04654243, -0.02011676, 0.000977798, 0.01855881, 0.033651089)
ff <- c(-0.10343798, -0.07416114, -0.05111547, -0.032481132, -0.01683215, -0.003636035)
gg <- c(-0.12237798, -0.09753544, -0.07785126, -0.061607548, -0.04788856, -0.036169540)
hh <-rbind(aa,bb,cc,dd,ee,ff,gg)
z <- as.matrix(hh)
y <- seq(0.5,1.75,0.25)
x <- seq(1,2.5,0.25)
filled.contour(x,y,z,
key.title = title(main=expression("log"(lambda))),
color.palette = topo.colors) #This works
contour(x,y,z, level=0,add=T,lwd=3) #This line doesn't match plot
This is completely answered in the ?filled.contour help page. In the Notes section it states
The output produced by filled.contour is actually a combination of two plots; one is the filled contour and one is the legend. Two separate coordinate systems are set up for these two plots, but they are only used internally – once the function has returned these coordinate systems are lost. If you want to annotate the main contour plot, for example to add points, you can specify graphics commands in the plot.axes argument. See the examples.
And the examples given in that help page show how to annotate on top of the main plot. In this particular case, the correct way would be
filled.contour(x,y,z,
key.title = title(main=expression("log"(lambda))),
color.palette = topo.colors,
plot.axes = {
axis(1)
axis(2)
contour(x,y,z, level=0,add=T,lwd=3)
}
)
which produces
So I am trying to plot two p values from two different data frames and compare them to the normal distribution in QQplot in R
here is the code that I am using
## Taking values from 1st dataframe to plot
Rlogp = -log10(trialR$PVAL)
Rindex <- seq(1, nrow(trialR))
Runi <- Rindex/nrow(trialR)
Rloguni <- -log10(Runi)
## Taking values from 2nd dataframe to plot on existing plot
Nlogp = -log10(trialN$PVAL)
Nlogp = sort(Nlogp)
Nindex <- seq(1, nrow(trialN))
Nuni <- Nindex/nrow(trialN)
Nloguni <- -log10(Nuni)
Nloguni <- sort(Nloguni)
qqplot(Rloguni, Rlogp, xlim=range(0,6), ylim=range(0,6), col=rgb(100,0,0,50,maxColorValue=255), pch=19, lwd=2, bty="l",xlab ="", ylab ="")
qqline(Rloguni, Rlogp,distribution=qnorm, lty="dashed")
par(new=TRUE, cex.main=4.8, col.axis="white")
plot(Nloguni, Nlogp, xlim=range(0,6), ylim=range(0,6), col=rgb(0,0,100,50,maxColorValue=255), pch=19, lwd=2, bty="l",xlab ="", ylab ="")
The code plot the graph effectively,but I am not sure of the qqline as it seems bit offset... Can someone tell me if I am doing the correct way or is there something to change
the TARGET plot will look something like this - without the third data value..
A minor question about plotting stacked barplot in R.
The stacked bars represent the series bottom-to-top.
But the legend always shows the series top-to-bottom. I think that is also true with ggplot2::geom_bar
Is there any nicer idiom than using rev(...) twice inside either legend() or barplot() as in:
exports <- data.frame(100*rbind('Americas'=runif(6),'Asia'=runif(6),'Other'=runif(6)))
colnames(exports) <- 2004:2009
series_we_want <- c(1,2,3)
barplot( as.matrix(exports[series_we_want,]), col=mycolors, ...)
legend(x="topleft", legend=rev(rownames(exports)[series_we_want]), col=rev(mycolors) ...)
(If you omit one of the rev()'s the output is obviously meaningless. Seems like an enhance case for adding a single flag yflip=TRUE or yreverse=TRUE)
This is what I got using your code:
exports <- data.frame(100*rbind('Americas'=runif(6),'Asia'=runif(6),'Other'=runif(6)))
colnames(exports) <- 2004:2009
series_we_want <- c(1,2,3)
barplot( as.matrix(exports[series_we_want,]))
legend(x="topleft", legend=rev(rownames(exports)[series_we_want]))
try this:
exports <- data.frame(100*rbind('Americas'=runif(6),'Asia'=runif(6),'Other'=runif(6)))
colnames(exports) <- 2004:2009
series_we_want <- c(1,2,3)
test_data<-as.matrix(exports[series_we_want])
barplot( test_data,
legend.text=as.character(rev(rownames(exports)[series_we_want])),
args.legend = list(x="topleft"))
seems to produce the legend in the opposite order of what you have
I would like to plot a simple graphic. I have a dat set with n rowns and k columns, in which each row has a a sequence of 0 and 1. I would like to plot exactly this sequence for all rows.
Actually I want to reproduce the figure 24.1, p. 516, of Gelman and Hill's book (Data aAnalysis Using Regression and Multilevel/Hierarchical Models). I suspect that he made the graphic in Latex, but it seems quite ridiculous that I'm not able to repplicate this simple graphic in R. The figue is something like this. As you can see from the link, the "ones" are replaced by "S" and "zeros" by ".". It's a simple graphic, but it shows each individual response by time.
I would go with a formatted text output using sprintf. Much cleaner and simpler. If you still want a plot, you could go with the following:
Given matrix tbl containing your data:
tbl <- matrix(data=rep(0:1,25), nrow=5)
You can generate a plot as:
plot(1, 1, xlim=c(1,dim(tbl)[2]+.5), ylim=c(0.5,dim(tbl)[1]), type="n")
lapply(1:dim(tbl)[1], function(x) {
text(x=c(1:dim(tbl)[2]), y=rep(x,dim(tbl)[2]), labels=tbl[x,])
})
Using this as a base you can play around with the text and plot args to stylize the plot the way you wish.
Here are two possible solutions, based on fake data generated with this helper function:
generate.data <- function(rate=.3, dim=c(25,25)) {
tmp <- rep(".", prod(dim))
tmp[sample(1:prod(dim), ceiling(prod(dim)*rate))] <- "S"
m <- matrix(tmp, nr=dim[1], nc=dim[2])
return(m)
}
Text-based output
x <- generate.data()
rownames(x) <- colnames(x) <- 1:25
capture.output(as.table(x), file="res.txt")
The file res.txt include a pretty-printed version of the console output; you can convert it to pdf using any txt to pdf converter (I use the one from PDFlib). Here is a screenshot of the text file:
Image-based output
First, here is the plotting function I used:
make.table <- function(x, labels=NULL) {
# x = matrix
# labels = list of labels for x and y
coord.xy <- expand.grid(x=1:nrow(x), y=1:ncol(x))
opar <- par(mar=rep(1,4), las=1)
plot.new()
plot.window(xlim=c(0, ncol(x)), ylim=c(0, nrow(x)))
text(coord.xy$x, coord.xy$y, c(x), adj=c(0,1))
if (!is.null(labels)) {
mtext(labels[[1]], side=3, line=-1, at=seq(1, ncol(x)), cex=.8)
mtext(labels[[2]], side=2, line=-1, at=seq(1, nrow(x)), cex=.8, padj=1)
}
par(opar)
}
Then I call it as
make.table(x, list(1:25, 1:25))
and here is the result (save it as png, pdf, jpg, or whatever).
As far as I can see, this is a text table. I am wondering why you want to make it a graph? Anyway, quick solutions are (either way)
make the text table (by programming or typing) and make its screenshot and embed the image into the plot.
make a blank plot and put the text on the plot by programming R with "text" function. For more info on "text", refer to http://cran.r-project.org/doc/contrib/Lemon-kickstart/kr_adtxt.html