Related
Update- this issue was solved, updated code is at the end of the post.
I am trying to create a swimmer plot to visualize individual patient duration of treatment with a drug administered at multiple dose levels (DLs). Each patient will be be assigned to treatment with only one DL, but multiple patients can be assigned to a given DL (e.g. 3 patients at DL1, 3 patients and DL2, etc.). I would like to color code the bars in the swimmer plot according to DL.
I am using the swimplot package for R and have been following the guide located here (https://cran.r-project.org/web/packages/swimplot/vignettes/Introduction.to.swimplot.html).
This guide has been sufficient for most things I have tried, up until I tried to change the colors of the bars in the plot and corresponding legend. Following the section in that guide titled "Modifying Colours and shapes" under "Making the plots more aesthetically pleasing with ggplot manipulations", I was able to change the bar colors in the legend, but not the bars themselves.
Example here
I have been using the following code.
library(ggplot2)
library (swimplot)
library (gdata)
library (readxl)
ClinicalTrial.Arm <- read_excel("Swimmer_Test_Data1.xls")
ClinicalTrial.Arm <- as.data.frame(ClinicalTrial.Arm)
arm_plot <- swimmer_plot(df=ClinicalTrial.Arm,id='id',end='End_trt',width=.85+ scale_fill_manual(name="Arm",values=c("DL1" ="#003f5c", "DL2"="#374c80","DL3"="#7a5195","DL4"="#bc5090","DL5"="#ef5675","DL6"="#ff764a","DL7"="#ffa600"))+ scale_color_manual(name="Arm",values=c("DL1" ="#003f5c", "DL2"="#374c80","DL3"="#7a5195","DL4"="#bc5090","DL5"="#ef5675","DL6"="#ff764a","DL7"="#ffa600"))
arm_plot
I have tried a number of things to fix this, but am quite new to R and don't think I really know enough to troubleshoot effectively. I have tried various syntax changes (e.g. removing quotation marks) and have tried using the geom bar command but wasn't sure how/what to map to X and Y (it also seems like I shouldn't need to do this).
I have also tried using the following code, but get an error.
Colors <- c("DL1" ="#003f5c", "DL2"="#374c80","DL3"="#7a5195","DL4"="#bc5090","DL5"="#ef5675","DL6"="#ff764a","DL7"="#ffa600")
arm_plot <- swimmer_plot(df=ClinicalTrial.Arm,id='id',end='End_trt',width=.85, fill = Colors)+ scale_fill_manual(name="Arm",values=c("DL1" ="#003f5c", "DL2"="#374c80","DL3"="#7a5195","DL4"="#bc5090","DL5"="#ef5675","DL6"="#ff764a","DL7"="#ffa600"))+ scale_color_manual(name="Arm",values=c("DL1" ="#003f5c", "DL2"="#374c80","DL3"="#7a5195","DL4"="#bc5090","DL5"="#ef5675","DL6"="#ff764a","DL7"="#ffa600"))
Error in `check_aesthetics()`:
! Aesthetics must be either length 1 or the same as the data (20): fill
Run `rlang::last_error()` to see where the error occurred.
Any help here would be greatly appreciated.
Solved! Updated, working code
library(ggplot2)
library (swimplot)
library (gdata)
library (readxl)
ClinicalTrial.Arm <- read_excel("Swimmer_Test_Data1.xls")
ClinicalTrial.Arm <- as.data.frame(ClinicalTrial.Arm)
Colors <- c("DL1" ="#003f5c", "DL2"="#374c80","DL3"="#7a5195","DL4"="#bc5090","DL5"="#ef5675","DL6"="#ff764a","DL7"="#ffa600")
arm_plot <- swimmer_plot(df=ClinicalTrial.Arm,id='id',end='End_trt', name_fill = "Arm", width=.85) + scale_fill_manual(name="Arm",values = Colors) +
scale_color_manual(name="Arm",values=Colors)
To make your code work you first have to map a variable on the fill aesthetic which using swimplot could be achieved via the name_fill argument:
Note: As I use the ClinicalTrial.Arm dataset from the swimplot package I adjusted your color palette to make it work with the three categories of the Arm column in this dataset.
library(ggplot2)
library(swimplot)
#pal <- c("DL1" = "#003f5c", "DL2" = "#374c80", "DL3" = "#7a5195", "DL4" = "#bc5090", "DL5" = "#ef5675", "DL6" = "#ff764a", "DL7" = "#ffa600")
pal <- c("Arm A" = "#003f5c", "Arm B" = "#bc5090", "Off Treatment" = "#ffa600")
swimmer_plot(df = ClinicalTrial.Arm, id = "id", end = "End_trt", name_fill = "Arm", width = .85) +
scale_fill_manual(name = "Arm", values = pal)
I'm wondering if there is a way to embed external links within a plotly plot (specifically I'm using the plotly package in R, but I don't have to). I want to be able to click on points in a scatter plot and have that take me to an external page with more detailed information about that point. Below is a fake example to demonstrate the idea.
Also, if this is not possible in plotly, but someone knows another library that could do this, I would love to know about that too! Thanks in advance.
THE EXAMPLE:
Imagine we're plotting the distances of each cruise taken by ships owned by two different cruise lines. The code below makes a plot which shows all the voyages and, when you hover over a point, it shows you the name of the ship that took that voyage. What I want is to be able to click on a point and have it take me to some web page with, for example, a detailed log of that particular voyage. (This is all a fake example, these logs don't actually exist.) Another sidenote: I'm using ggplotly because I'm comfortable with ggplot2 but if there's a way to do this in plot_ly I'm happy to use that.
library(ggplot2)
library(plotly)
shipNames <- c("Princess", "Voyager", "Paul Simon", "Dangelo", "Virginia", "Meade", "Capt America", "Naw Dawg")
set.seed(1)
cruise <- data.frame(company = sample(c("Carnival", "Norweigen"), 20, replace = T),
shipName = sample(shipNames, 20, replace=T),
date = sample(seq(from=as.Date('2016-01-01'), to=as.Date('2016-12-31'), by=1), 20),
distance = sample(seq(from=300, to=500, by=1), 20)
)
g <- ggplot(cruise, aes(x=date, y=distance, colour=company, name = shipName)) + geom_point()
# you have to put the geom_line first or it fucks it up
g <- ggplot(cruise, aes(x=date, y=distance)) + geom_line(aes(colour=company)) + geom_point(aes(colour=company, name = shipName))
ggplotly(g, tooltip = c("x", "name"))
I've been trying to draw two plots using R's ggplot library in RStudio. Problem is, when I draw two within one function, only the last one displays (in RStudio's "plots" view) and the first one disappears. Even worse, when I run ggsave() after each plot - which saves them to a file - neither of them appear (but the files save as expected). However, I want to view what I've saved in the plots as I was able to before.
Is there a way I can both display what I'll be plotting in RStudio's plots view and also save them? Moreover, when the plots are not being saved, why does the display problem happen when there's more than one plot? (i.e. why does it show the last one but not the ones before?)
The code with the plotting parts are below. I've removed some parts because they seem unnecessary (but can add them if they are indeed relevant).
HHIplot = ggplot(pergame)
# some ggplot geoms and misc. here
ggsave(paste("HHI Index of all games,",year,"Finals.png"),
path = plotpath, width = 6, height = 4)
HHIAvePlot = ggplot(AveHHI, aes(x = AveHHI$n_brokers))
# some ggplot geoms and misc. here
ggsave(paste("Average HHI Index of all games,",year,"Finals.png"),
path = plotpath, width = 6, height = 4)
I've already taken a look here and here but neither have helped. Adding a print(HHIplot) or print(HHIAvePlot) after the ggsave() lines has not displayed the plot.
Many thanks in advance.
Update 1: The solution suggested below didn't work, although it works for the answer's sample code. I passed the ggplot objects to .Globalenv and print() gives me an empty gray box on the plot area (which I imagine is an empty ggplot object with no layers). I think the issue might lie in some of the layers or manipulators I have used, so I've brought the full code for one ggplot object below. Any thoughts? (Note: I've tried putting the assign() line in all possible locations in relation to ggsave() and ggplot().)
HHIplot = ggplot(pergame)
HHIplot +
geom_point(aes(x = pergame$n_brokers, y = pergame$HHI)) +
scale_y_continuous(limits = c(0,10000)) +
scale_x_discrete(breaks = gameSizes) +
labs(title = paste("HHI Index of all games,",year,"Finals"),
x = "Game Size", y = "Herfindahl-Hirschman Index") +
theme(text = element_text(size=15),axis.text.x = element_text(angle = 0, hjust = 1))
assign("HHIplot",HHIplot, envir = .GlobalEnv)
ggsave(paste("HHI Index of all games,",year,"Finals.png"),
path = plotpath, width = 6, height = 4)
I'll preface this by saying that the following is bad practice. It's considered bad practice to break a programming language's scoping rules for something as trivial as this, but here's how it's done anyway.
So within the body of your function you'll create both plots and put them into variables. Then you'll use ggsave() to write them out. Finally, you'll use assign() to push the variables to the global scope.
library(ggplot2)
myFun <- function() {
#some sample data that you should be passing into the function via arguments
df <- data.frame(x=1:10, y1=1:10, y2=10:1)
p1 <- ggplot(df, aes(x=x, y=y1))+geom_point()
p2 <- ggplot(df, aes(x=x, y=y2))+geom_point()
ggsave('p1.jpg', p1)
ggsave('p2.jpg', p2)
assign('p1', p1, envir=.GlobalEnv)
assign('p2', p2, envir=.GlobalEnv)
return()
}
Now, when you run myFun() it will write out your two plots to .jpg files, and also drop the plots into your global environment so that you can just run p1 or p2 on the console and they'll appear in RStudio's Plot pane.
ONCE AGAIN, THIS IS BAD PRACTICE
Good practice would be to not worry about the fact that they're not popping up in RStudio. They wrote out to files, and you know they did, so go look at them there.
I'm attempting to step through a dataset and create a histogram and summary table for each factor and save the output as a .svg . The histogram is created using ggplot2 and the summary table using summary().
I have successfully used the code below to save the output to a single .pdf with each page containing the relevant histogram/table. However, when I attempt to save each histogram/table combo into a set of .svg images using ggsave only the ggplot histogram is showing up in the .svg. The table is just white space.
I've tried using dev.copy Cairo and svg but all end up with the same result: Histogram renders, but table does not. If I save the image as a .png the table shows up.
I'm using the iris data as a reproducible dataset. I'm not using R-Studio which I saw was causing some "empty plot" grief for others.
#packages used
library(ggplot2)
library(gridExtra)
library(gtable)
library(Cairo)
#Create iris histogram plot
iris.hp<-ggplot(data=iris, aes(x=Sepal.Length)) +
geom_histogram(binwidth =.25,origin=-0.125,
right = TRUE,col="white", fill="steelblue4",alpha=1) +
labs(title = "Iris Sepal Length")+
labs(x="Sepal Length", y="Count")
iris.list<-by(data = iris, INDICES = iris$Species, simplify = TRUE,FUN = function(x)
{iris.hp %+% x + ggtitle(unique(x$Species))})
#Generate list of data to create summary statistics table
sum.str<-aggregate(Sepal.Length~Species,iris,summary)
spec<-sum.str[,1]
spec.stats<-sum.str[,2]
sum.data<-data.frame(spec,spec.stats)
sum.table<-tableGrob(sum.data)
colnames(sum.data) <-c("species","sep.len.min","sep.len.1stQ","sep.len.med",
"sep.len.mean","sep. len.3rdQ","sep.len.max")
table.list<-by(data = sum.data, INDICES = sum.data$"species", simplify = TRUE,
FUN = function(x) {tableGrob(x)})
#Combined histogram and summary table across multiple plots
multi.plots<-marrangeGrob(grobs=(c(rbind(iris.list,table.list))),
nrow=2, ncol=1, top = quote(paste(iris$labels$Species,'\nPage', g, 'of',pages)))
#bypass the class check per #baptiste
ggsave <- ggplot2::ggsave; body(ggsave) <- body(ggplot2::ggsave)[-2]
#
for(i in 1:3){
multi.plots<-marrangeGrob(grobs=(c(rbind(iris.list[i],table.list[i]))),
nrow=2, ncol=1,heights=c(1.65,.35),
top = quote(paste(iris$labels$Species,'\nPage', g, 'of',pages)))
prefix<-unique(iris$Species)
prefix<-prefix[i]
filename<-paste(prefix,".svg",sep="")
ggsave(filename,multi.plots)
#dev.off()
}
Edit removed theme tt3 that #rawr referenced. It was accidentally left in example code. It was not causing the problem, just in case anyone was curious.
Edit: Removing previous answer regarding it working under 32bit install and not x64 install because that was not the problem. Still unsure what was causing the issue, but it is working now. Leaving the info about grid.export as it may be a useful alternative for someone else.
Below is the loop for saving the .svg's using grid.export(), although I was having some text formatting issues with this (different dataset).
for(i in 1:3){
multi.plots<-marrangeGrob(grobs=(c(rbind(iris.list[i],table.list[i]))),
nrow=2, ncol=1,heights=c(1.65,.35), top =quote(paste(iris$labels$Species,'\nPage', g,
'of',pages)))
prefix<-unique(iris$Species)
prefix<-prefix[i]
filename<-paste(prefix,".svg",sep="")
grid.draw(multi.plots)
grid.export(filename)
grid.newpage()
}
EDIT: As for using arrangeGrob per #baptiste's comment. Below is the updated code. I was incorrectly using the single brackets [] for the returned by list, so I switched to the correct double brackets [[]] and used grid.draw to on the ggsave call.
for(i in 1:3){
prefix<-unique(iris$Species)
prefix<-prefix[i]
multi.plots<-grid.arrange(arrangeGrob(iris.list[[i]],table.list[[i]],
nrow=2,ncol=1,top = quote(paste(iris$labels$Species))))
filename<-paste(prefix,".svg",sep="")
ggsave(filename,grid.draw(multi.plots))
}
I am producing a stratigraphy plot which should look something like the following
I've got to the point where I can plot the layout of the plot using some dummy data and the following code
Strat <- c(657,657,657,657,657,657,657,657,657,657,601,601,601,601,601,601,601,601,601,601,610,610,610,610,610,610,610,610,610,610)
Distance <- c(7.87,17.89,22.09,42.84,50.65,55.00,65.74,69.38,72.36,75.31,7.87,17.89,22.09,42.84,50.65,55.00,65.74,69.38,72.36,75.31,7.87,17.89,22.09,42.84,50.65,55.00,65.74,69.38,72.36,75.31)
Altitude <- c(565.05,191.98,808.12,609.19,579.10,657.08,708.00,671.44,312.10,356.14,565.05,191.98,808.12,609.19,579.10,657.08,708.00,671.44,312.10,356.14,565.05,191.98,808.12,609.19,579.10,657.08,708.00,671.44,312.10,356.14)
strat_max <- c(565.05,191.98,808.12,609.19,579.10,657.08,708.00,671.44,312.10,356.14,565.04,176.23,795.52,608.06,567.89,641.83,698.69,664.50,310.21,350.11,526.47,147.30,762.49,601.99,544.22,632.54,689.33,636.40,282.71,313.56)
strat_min <- c(565.04,176.23,795.52,608.06,567.89,641.83,698.69,664.50,310.21,350.11,526.47,147.30,762.49,601.99,544.22,632.54,689.33,636.40,282.71,313.56,463.31,81.01,718.11,594.38,539.53,616.18,670.79,602.96,249.59,289.63)
strat <- cbind(Strat, Distance, Altitude, strat_max, strat_min)
strat <- as.data.frame(strat)
attach(strat)
ggplot(strat, aes(x=Distance, y=Altitude, colour=factor(Strat))) +
geom_linerange(aes(x=Distance, ymax=strat_max, ymin=strat_min, colour=factor(Strat)), lwd=10) +
geom_line(lty=1, lwd=1.5, colour="black") +
xlab("Distance") + ylab("Altitude") +
theme_bw() + scale_colour_discrete(name="Stratigraphy Type")
However, I have been unable to add the relevant patterns. Each rock/ sediment type has a standard plotting pattern for use in stratigraphic plots from the USGS and I would like to relate the code in strat$Strat to the relevant pattern and use that as the pattern
Does anyone know how to import these (e.g. as PNG files) and then use them as patterns? I had thought to try and call them as colours but I don't know if that would work and there's probably no framework for telling R how to repeat them. Currently I am writing the plot as shown and then adding in the patterns in adobe illustrator
Any insight appreciated!