I have a simple R-Script:
args <- commandArgs(TRUE)
inp <- read.csv(args[1],sep="\t",header=FALSE,stringsAsFactors=FALSE)
firstCol <- inp$V2
secondCol <- inp$V3
pdf(args[2])
plot(firstCol,secondCol,xlab="#",ylab="maxLength")
dev.off()
I run it from a bash script to generate a basic plot.
Now I want to use X11() to plot directly into a window and not into a PDF.
What I want now is to appear the label (in inp$V1) of every dot on the console when hovering over a point or klicking onto it.
How to do?
The identify function lets you click on points and it returns the index value for the points clicked on that could be used to subset a vector of labels.
For identification when hovering (instead of clicking) you can look at the HTKidentify function in the TeachingDemos package.
Edit
Here is an example using identify that may be more what you want (I tested it on windows, not unix/X11):
x <- runif(26)
y <- rnorm(26)
plot(x,y)
while(length(tmp <- identify(x,y, plot=FALSE, n=1))) {
cat(letters[tmp],'\n')
}
The plot=FALSE tells identify to not put the label on the plot and the n=1 tells it to return after you click on 1 point (the while goes back to identifying more points, but prints out the label immediately).
Obviously you would create other labels to use than just the letters.
Related
I have created one function that contains two types of plots and it will give you one image. However, the title of this image will change depending on one list, so, you will have several plots but different title.
(The original function will change the numbers that the plot uses but, in essence, is what I need).
This is the example that I have created.
list_genes <- c("GEN1", "GEN2", "GEN3")
myfunction <- function(x,y){
for(gene in list_genes){
# This to draw both plots
par(mfrow=c(2,1))
plot(x,y, main=paste0("Plot of ", gene))
hist(x, main=paste0("Plot of ", gene))
}
}
myfunction(x=c(1,5,6,2,4),y=c(6,10,53,1,5))
Since the list has 3 elements, we get 3 plots.
However, as I need to create a presentation with all the plots that I generate, I found this post with a solution to create slides for several plots inside a for loop. It is what I want, but for that, I need to save my plots into a list/variable.
object <- myfunction(x=c(1,5,6,2,4),y=c(6,10,53,1,5))
> object
NULL
I found this post (which gives you an interesting solution) but, the plots still cannot be saved into an object.
calling_myfunc <- function(){
myfunction(x=c(1,5,6,2,4),y=c(6,10,53,1,5))
}
calling_myfunc()
object <- calling_myfunc()
> object
NULL
My final objective is to create a presentation (automatically) with all of the plots that I generate from my function. As I saw in this post. But I need to save the plots into a variable.
Could anyone help me with this?
Thanks very much in advance
Although I couldn't find the way to save the plots into an object, I found a way to create a presentation with those images thanks to this post and the export package.
library(export)
list_genes <- c("GEN1", "GEN2", "GEN3")
myfunction <- function(x,y){
for(gene in list_genes){
# This to draw both plots
par(mfrow=c(2,1))
plot(x,y, main=paste0("Plot of ", gene))
hist(x, main=paste0("Plot of ", gene))
graph2ppt(file="plots.pptx", width=6, height=5,append=TRUE) } }
myfunction(x=c(1,5,6,2,4),y=c(6,10,53,1,5))
Of course, the width and height of the plots can be changed or put them as a parameter in the function.
Since the package is not available in CRAN for my current R version (4.1.2), I downloaded it from GitHub:
devtools::install_github("tomwenseleers/export")
In addition, I have found another package that I can use for the same purpose (although it adds one extra slide at the beginning, I don't know why)
library(eoffice)
list_genes <- c("GEN1", "GEN2", "GEN3")
myfunction <- function(x,y){
for(gene in list_genes){
# This to draw both plots
par(mfrow=c(2,1))
plot(x,y, main=paste0("Plot of ", gene))
hist(x, main=paste0("Plot of ", gene))
topptx(file="plots.pptx", width=6, height=5,append=TRUE)
}
}
myfunction(x=c(1,5,6,2,4),y=c(6,10,53,1,5))
PS: I found the solution to create a presentation --> How to create a presentation in R with several plots obtained by a function?
I have found that the beanplot is the best way to represent my data. I want to look at multiple beanplots together to visualize my data. Each of my plots contains 3 variables, so each one looks something like what would be generated by this code:
library(beanplot)
a <- rnorm(100)
b <- rnorm(100)
c <- rnorm(100)
beanplot(a, b ,c ,ylim = c(-4, 4), main = "Beanplot",
col = c("#CAB2D6", "#33A02C", "#B2DF8A"), border = "#CAB2D6")
(Would have just included an image but my reputation score is not high enough, sorry)
I have 421 of these that I want to put into one long PDF (EDIT: One plot per page is fine, this was just poor wording on my part). The approach I have taken was to first generate the beanplots in a for loop and store them in a list at each iteration. Then I will use the multiplot function (from the R Cookbook page on multiplot) to display all of my plots on one long column so I can begin my analysis.
The problem is that the beanplot function does not appear to be set up to assign plot objects as a variable. Example:
library(beanplot)
a <- rnorm(100)
b <- rnorm(100)
plot1 <- beanplot(a, b, ylim = c(-5,5), main = "Beanplot",
col = c("#CAB2D6", "#33A02C", "#B2DF8A"), border = "#CAB2D6")
plot1
If you then type plot1 into the R console, you will get back two of the plot parameters but not the plot itself. This means that when I store the plots in the list, I am unable to graph them with multiplot. It will simply return the plot parameters and a blank plot.
This behavior does not seem to be the case with qplot for example which will return a plot when you recall the stored plot. Example:
library(ggplot2)
a <- rnorm(100)
b <- rnorm(100)
plot2 <- qplot(a,b)
plot2
There is no equivalent to the beanplot that I know of in ggplot. Is there some sort of workaround I can use for this issue?
Thank you.
You can simply open a PDF device with pdf() and keep the default parameter onefile=TRUE. Then call all your beanplot()s, one after the other. They will all be in one PDF document, each one on a separate page. See here.
In a scatterplot, I would like to use identify function to label the right top point.
I did this:
identify(x, y, labels=name, plot=TRUE)
*I have a named vector.
Then, while it is running, I point to the right point. Then after stopping it, it shows me the
label of the point.
Do I have to click the point that I want to label each time? Can I save it?
# Here is an example
x = 1:10
y = x^2
name = letters[1:10]
plot(x, y)
identify(x, y, labels = name, plot=TRUE)
# Now you have to click on the points and select finish at the end
# The output will be the labels you have corresponding to the dots.
Regarding saving it:
I couldn't do it using
pdf()
# plotting code
dev.off()
However in Rstudio it was posible to "copy-paste" it. If you need one plot only, i guess this would work.
You can use the return value of identify function to reproduce the labelling:
labels <- rep(letters, length.out=nrow(cars))
p <- identify(cars$speed, cars$dist, labels, plot=T)
#now we can reproduce labelling
plot(cars)
text(cars$speed[p], cars$dist[p], labels[p], pos=3)
To save the plot after using identify, you can use dev.copy:
labels <- rep(letters, length.out=nrow(cars))
identify(cars$speed, cars$dist, labels, plot=T)
#select your points here
dev.copy(png, 'myplot.png', width=600, height=600)
dev.off()
I have the following example
data(diamonds, package="ggplot2")
diamonds.samp <- diamonds[sample(1:dim(diamonds)[1],200),]
ggpairs(diamonds.samp, columns=8:10,
upper=list(continuous='cor'),
lower=list(continuous = 'points'),
diag=list(continuous='density'),
axisLabels='show'
)
Resulting in a really nice figure:
But my problem is that in the real dataset I have to many points whereby I would like to change the parameters for the point geom. I want to reduce the dot size and use a lower alpha value. I can however not doe this with the "param" option it applies to all plot - not just the lower one:
ggpairs(diamonds.samp, columns=8:10,
upper=list(continuous='cor'),
lower=list(continuous = 'points'),
diag=list(continuous='density'),
params=c(alpha=1/10),
axisLabels='show'
)
resulting in this plot:
Is there a way to apply parameters to only "lower" plots - or do I have to use the ability to create custom plots as suggested in the topic How to adjust figure settings in plotmatrix?
In advance - thanks!
There doesn't seem to be any elegant way to do it, but you can bodge it by writing a function to get back the existing subchart calls from the ggally_pairs() object and then squeezing the params in before the last bracket. [not very robust, it'll only work for if the graphs are already valid]
diamonds.samp <- diamonds[sample(1:dim(diamonds)[1],200),]
g<-ggpairs(diamonds.samp, columns=8:10,
upper=list(continuous='cor'),
lower=list(continuous = 'points'),
diag=list(continuous='density'),
axisLabels='show'
)
add_p<-function(g,i,params){
side=length(g$columns) # get number of cells per side
lapply(i,function(i){
s<-as.character(g$plots[i]) # get existing call as a template
l<-nchar(s)
p<-paste0(substr(s,1,l-1),",",params,")") # append params before last bracket
r<-i%/%side+1 # work out the position on the grid
c<-i%%side
array(c(p,r,c)) # return the sub-plot and position data
})
}
rep_cells<-c(4,7,8)
add_params<-"alpha=0.3, size=0.1, color='red'"
ggally_data<-g$data # makes sure that the internal parameter picks up your data (it always calls it's data 'ggally_data'
calls<-add_p(g,rep_cells,params=add_params) #call the function
for(i in 1:length(calls)){g<-putPlot(g,calls[[i]][1],as.numeric(calls[[i]][2]),as.numeric(calls[[i]][3]))}
g # call the plot
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.