I have a list of plots that I have assigned names to, and then converted to plot titles as suggested by https://stackoverflow.com/a/14790376/9335733. The titles happen to appear over the top x-axis title and so I attempt to move them as suggested here: https://stackoverflow.com/a/44618277/9335733. The overall code looks as follows:
lapply(names(Cast.files), function (x) plot(Cast.files[[x]],
main = x,
adj = 0, #adjust title to the farthest left
line =2.5 #adjust title up 2.5
)
)
It should be noted that plot is now converted from base R to the oce package for analyzing oceanographic data, but calls the same arguments from base R plot.
The problem becomes that in trying to move the title, the axis labels move as well and overlap. Any suggestions?
Edit: Here is what the image looks like before:
And after:
You might also want to look into the oma= argument in par(), which provides an "outer" margin which can be used to put a nice title. Something like:
library(oce)
data(ctd)
par(oma=c(0, 0, 1, 0))
plot(ctd)
title('Title', outer=TRUE)
This was solved by adding a title argument outside of the plot function as follows:
lapply(names(Cast.files), function (x) plot(Cast.files[[x]],
which = c("temperature", "salinity", "sigmaT","conductivity"),
Tlim = c(11,12),
Slim = c(29,32),
col = "red")
+ title(main = x, adj = 0.48, line = 3.5)#adding the titles at a specific location
)
This allowed for plots that looked like:
If you use the title function, rather than setting main within plot, it would allow you to change the line without affecting anything else in the plot.
Related
I want to remove or rename the "top axis title" of the following plot based on the package plotmo. Here is a short reproducible example:
library(glmnet)
library(plotmo)
data(mtcars)
fit <- glmnet(x=as.matrix(mtcars[,-1]), y=as.matrix(mtcars[,1]))
plot_glmnet(fit)
Results in:
It looks like, that the plot is made by base plot functions. May someone knows a way to Change the top axis title or remove it
The only way I could achieve what you desire is by editing the source code.
plot_glmet.edited<- plot_glmnet ## copy the function
as.list(body(plot_glmet.edited)) ## print the lines of the function
At the moment the code will not print a label, replace NA with any character string that you want as a title
body(plot_glmet.edited)[[33]] <- substitute(
mtext(NA, side = 3, line = 1.5, cex = par("cex") * par("cex.lab")))
How to create multiple boxplot with value shown in R ?
Now I'm using this code
boxplot(Data_frame[ ,2] ~ Data_frame[ ,3], )
I tried to use this
boxplot(Data_frame[ ,2] ~ Data_frame[ ,3], )
text(y=fivenum(Data_frame$x), labels =fivenum(Data_frame$x), x=1.25)
But only first boxplot have value. How to show value in all boxplot in one graph.
Thank you so much!
As far as I understand your question (it is not clear how the fivenum summary should be displayed) here is one solution. It presents the summary using the top axis.
x <- data.frame(
Time = c(1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,3,3,3,3,3,3,3,3),
Value = c(5,10,15,20,30,50,70,80,100,5,7,9,11,15,17,19,17,19,100,200,300,400,500,700,1000,200))
boxplot(x$Value ~ x$Time)
fivenums <- aggregate(x$Value, by=list(Time=x$Time), FUN=fivenum)
labels <- apply(fivenums[,-1], 1, function(x) paste(x[-1], collapse = ", "))
axis(3, at=fivenums[,1],labels=labels, las=1, col.axis="red")
Of course you can additionally play with the font size or rotation for this summary. Moreover you can break the line in one place, so the label will have smaller width.
Edit
In order to get what have you posted in the comment below you can add
text(x = 3 + 0.5, y = fivenums[3,-1], labels=fivenums[3,-1])
and you will get
however it won't be readable for other boxplots.
I'm still relatively inexperienced manipulating plots in R, and am in need of assistance. I ran a redundancy analysis in R using the rda() function, but now I need to simplify the figure to exclude unnecessary information. The code I'm currently using is:
abio1516<-read.csv("1516 descriptors.csv")
attach(abio1516)
bio1516<-read.csv("1516habund.csv")
attach(bio1516)
rda1516<-rda(bio1516[,2:18],abio1516[,2:6])
anova(rda1516)
RsquareAdj(rda1516)
summary(rda1516)
varpart(bio1516[,2:18],~Distance_to_source,~Depth, ~Veg._cover, ~Surface_area,data=abio1516)
plot(rda1516,bty="n",xaxt="n",yaxt="n",main="1516; P=, R^2=",
ylab="Driven by , Var explained=",xlab="Driven by , Var explained=")
The produced plot looks like this:
Please help me modify my code to: exclude the sites (sit#), all axes, and the internal dashed lines.
I'd also like to either expand the size of the field, or move the vector labels to all fit in the plotting field.
updated as per responses, working code below this point
plot(rda,bty="n",xaxt="n",yaxt="n",type="n",main="xxx",ylab="xxx",xlab="xxx
Overall best:xxx")
abline(h=0,v=0,col="white",lwd=3)
points(rda,display="species",col="blue")
points(rda,display="cn",col="black")
text(rda,display="cn",col="black")
Start by plotting the rda with type = "n" which generates an empty plot to which you can add the things you want. The dotted lines are hard coded into the plot.cca function, so you need either make your own version, or use abline to hide them (then use box to cover up the holes in the axes).
require(vegan)
data(dune, dune.env)
rda1516 <- rda(dune~., data = dune.env)
plot(rda1516, type = "n")
abline(h = 0, v = 0, col = "white", lwd = 3)
box()
points(rda1516, display = "species")
points(rda1516, display = "cn", col = "blue")
text(rda1516, display = "cn", col = "blue")
If the text labels are not in the correct position, you can use the argument pos to move them (make a vector as long as the number of arrows you have with the integers 1 - 4 to move the label down, left, up, or right. (there might be better solutions to this)
I would like the title to be centered above the two plots in my mfrow object. Indeed, I have just that working, but the title is too far above the plots, and is only half included because of this. Below is my code showing the issue. How can I move the title down to just above the plots in the center?
a=1
p = c(rnorm(1000,5,10))
l = c(rnorm(1000,10,5))
par(mfrow=c(1,2))
hist(p,main=NULL)
hist(l,main=NULL)
title(main=print(paste0("Histogram a=", a)),outer=T)
If you set the line parameter in the title call to, for example, -2, you can place the title closer to the histograms:
a=1
p = c(rnorm(1000,5,10))
l = c(rnorm(1000,10,5))
par(mfrow=c(1,2))
hist(p,main=NULL)
hist(l,main=NULL)
title(main=print(paste0("Histogram a=", a)),outer=T, line=-2)
I am creating violin plots with lots (will be ~100) of columns (violins). The problem is that the name of each column is very long. What I am doing current is as follows:
jpeg("stats/AllDistanceViolinPlot.jpg", width = 1000, height = 1000);
do.call(vioplot, c(lapply(data, na.omit),list(names=c("veryveryveryverylongname1", "veryveryveryverylongname2", "veryveryveryverylongname4", "veryveryveryverylongname4", "veryveryveryverylongname5", "veryveryveryverylongname6", "veryveryveryverylongname7", "veryveryveryverylongname8"))));
dev.off()
Which gives me this plot:
As you can see, the names of the columns are very long and some actually are not shown. I have also tried something without the list:
jpeg("stats/plot.jpg", width = 1000, height = 1000);
do.call(vioplot, c(lapply(data, na.omit)));
dev.off()
Which gives me this plot:
What I'd like is one of two things:
The names of the columns would be vertical so that they are shown and aren't cut off
or
Make the main plot like the second image I posted and have a separate legend that would correlate each column with the full name. For example, something like the following:
1 - veryveryveryverylongname1
2 - veryveryveryverylongname2
...
8 - veryveryveryverylongname8
Could someone please suggest the better way (or both) and comment on how to implement them?
Greatly appreciated.
Unfortunately the vioplot function in the vioplot package does not accept the usual base graphics parameters for modifying the orientation of axis annotation. You will need to make a new vioplot function and change this code:
if (!horizontal) {
if (!add) {
plot.window(xlim = xlim, ylim = ylim)
axis(2)
axis(1, at = at, label = label)
To this:
if (!horizontal) {
if (!add) {
plot.window(xlim = xlim, ylim = ylim)
axis(2)
axis(1, at = at, label = label , las=2)