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• Annotating axis in ggplot2

  - by mpiktas

  I am looking for the way to annotate axis in ggplot2. The example of the problem can be found here: http://learnr.wordpress.com/2009/09/24/ggplot2-back-to-back-bar-charts. The y axis of the chart (example graph in the link) has an annotation: (million euro). Is there a way to create such types of annotations in ggplot2? Looking at the documentation there is no obvious way, since the ggplot does not explicitly let you put objects outside plotting area. But maybe there is some workaround? One of the possible workarounds I thought about is using scales: data=data.frame(x=1:10,y=1:10) qplot(x=x,y=y,data=data)+scale_y_continuous(breaks=10.1,label="Millions") But then how do I remove the tick? And it seems that since ggplot does not support multiple scales, I will need to grab the output of the scale_y_continuous, when it calculates the scales automaticaly and then add my custom break and label by hand. Maybe there is a better way?

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• Move a legend in ggplot2

  - by Dan Goldstein

  I'm trying to create a ggplot2 plot with the legend beneath the plot. The ggplot2 book says on p 112 "The position and justification of legends are controlled by the theme setting legend.position, and the value can be right, left, top, bottom, none (no legend), or a numeric position". The following code works (since "right" it is the default), and it also works with "none" as the legend position, but "left", "top", "bottom", all fail with "Error in grid.Call.graphics("L_setviewport", pvp, TRUE) : Non-finite location and/or size for viewport" library(ggplot2) (myDat <- data.frame(cbind(VarX=10:1, VarY=runif(10)), Descrip=sample(LETTERS[1:3], 10, replace=TRUE))) qplot(VarX,VarY, data=myDat, shape=Descrip) + opts(legend.position="right") What am I doing wrong? Re-positioning a legend must be incredibly common, so I figure it's me.

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• How safe am I singing into Google Spreadsheets with yeroon.net/ggplot2

  - by Farrel

  I am impressed by what I have seen of yeroon.net/ggplot2 which is a web interface for Hadley Wickham's R package ggplot2. I want to try it out on my own data. The part that has me very excited is that one can use data stored in one's own Google spreadsheet as the data. One just signs into their Google Account so that yeroon.net/ggplot2 can access the spreadsheet list. I have been hesitant to do it. If I sign in whilst on yeroon.net am I handing over my username and password to a third party? It would not be wise of me to divulge my google password to third parties since Google is fast becoming my repository of everything. How do I know if Jeroon's application is using ClientLogin or OAuth? My understanding is very basic and may be wrong but nevertheless here it is. OAuth would be better since it does not actually pass the password onto the third party application.

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• How to move or position a legend in ggplot2

  - by Dan Goldstein

  I'm trying to create a ggplot2 plot with the legend beneath the plot. The ggplot2 book says on p 112 "The position and justification of legends are controlled by the theme setting legend.position, and the value can be right, left, top, bottom, none (no legend), or a numeric position". The following code works (since "right" it is the default), and it also works with "none" as the legend position, but "left", "top", "bottom", all fail with "Error in grid.Call.graphics("L_setviewport", pvp, TRUE) : Non-finite location and/or size for viewport" library(ggplot2) (myDat <- data.frame(cbind(VarX=10:1, VarY=runif(10)), Descrip=sample(LETTERS[1:3], 10, replace=TRUE))) qplot(VarX,VarY, data=myDat, shape=Descrip) + opts(legend.position="right") What am I doing wrong? Re-positioning a legend must be incredibly common, so I figure it's me.

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• Help understanding how to make a bar chart using ggplot2

  - by celenius

  I'm trying to use the bar_geom function of ggplot2, but I can't understand how to use it. I've made a small sample of my code to show what I am trying to do: library(ggplot2) # sample data sampleData = data.frame( v1=c('a','b','c','d','e', 'f','g', 'h', 'i','j'), v2=c(1:10) ) sampleData$Names = data.frame( Names = paste(sampleData$v1, sampleData$v2, sep="") ) sampleData$Values = c(1:10) # make plot x = sampleData$Values y = sampleData$Names qplot( x, y, data = sampleData, geom="bar" ) I want sampleData$Names to be on the x-axis of my graph, labeling each bar and and sampleData$Values to scale the bar height. I want the y-axis to be specified as a range. I realize that I don't understand how ggplot2 functions as this small example does not work, yet my other example is generating a plot but I cannot specify a y-range as it considers the variables to be categorical.

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• How safe am I signing into Google Spreadsheets with yeroon.net/ggplot2

  - by Farrel

  I am impressed by what I have seen of yeroon.net/ggplot2 which is a web interface for Hadley Wickham's R package ggplot2. I want to try it out on my own data. The part that has me very excited is that one can use data stored in one's own Google spreadsheet as the data. One just signs into their Google Account so that yeroon.net/ggplot2 can access the spreadsheet list. I have been hesitant to do it. If I sign in whilst on yeroon.net am I handing over my username and password to a third party? It would not be wise of me to divulge my google password to third parties since Google is fast becoming my repository of everything. How do I know if Jeroon's application is using ClientLogin or OAuth? My understanding is very basic and may be wrong but nevertheless here it is. OAuth would be better since it does not actually pass the password onto the third party application.

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• ggplot2 footnote

  - by user338714

  What is the best way to add a footnote to the bottom of a plot created with ggplot2? I've tried using a combination of the logic noted here http://www.r-bloggers.com/r-good-practice-%E2%80%93-adding-footnotes-to-graphics/ as well as the ggplot2 annotate function p + annotate("text",label="Footnote", x=unit(1,"npc") - unit(2, "mm"),y=unit(2, "mm"), just=c("right", "bottom"),gp=gpar(cex= 0.7, col=grey(.5))) but I am getting the error "Error in as.data.frame.default(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) : cannot coerce class c("unit.arithmetic", "unit") into a data.frame".

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• Remove a layer from a ggplot2 chart

  - by Erik Shilts

  I'd like to remove a layer (in this case the results of geom_ribbon) from a ggplot2 created grid object. Is there a way I can remove it once it's already part of the object? library(ggplot2) dat <- data.frame(x=1:3, y=1:3, ymin=0:2, ymax=2:4) p <- ggplot(dat, aes(x=x, y=y)) + geom_ribbon(aes(ymin=ymin, ymax=ymax), alpha=0.3) + geom_line() # This has the geom_ribbon p # This overlays another ribbon on top p + geom_ribbon(aes(ymin=ymin, ymax=ymax, fill=NA))

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• How to override ggplot2's axis formatting?

  - by Richie Cotton

  When you choose a log scale, ggplot2 formats the breaks like 10^x. I'd like it to not do that. For example, the code below should display a graph with ticks at 1, 2, 5 etc, not 10^0, 10^0.3, 10^0.69 etc. library(ggplot2) dfr <- data.frame(x = 1:100, y = rlnorm(100)) breaks <- as.vector(c(1, 2, 5) %o% 10^(-1:1)) p1 <- ggplot(dfr, aes(x, y)) + geom_point() + scale_y_log10(breaks = breaks) print(p1) I guess that adding a formatter argument to scale_y_log10 would do the trick, but I'm not sure what to put in the argument, or where the options might be documented.

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• missing plot title in ggplot2

  - by Ben Mazzotta

  How can I create a plot title in ggplot2? Am I making a silly syntax error? The ggplot2 docs indicate that labs(title = 'foo') should work, but I can only get the arguments x='foo' and y='foo' to work with labs(). Neither ggtitle() nor title() worked either. Here is an example. x <- rnorm(10,10,1) y <- rnorm(10,20,2) xy.df <- data.frame(x,y) qplot(x,y, data=xy.df, geom='point', color=x*y) + labs(title = "New Plot Title", x='Some Data', y='Some Other Data')

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• plot only x and y axis (no box) in ggplot2

  - by Tyler Rinker

  The convention of some journals is to show only the x and y axis in a plot not a box around the entire plot area. How can I achieve this in ggplot2? I tried theme_minimal_cb_L from HERE but it seems to erase the entire box around the plot (does not leave the x and y axis) as seen here: Here's the code I'm using: dat <- structure(list(x = c(0.7, 0.75, 0.8, 0.85, 0.9, 0.95, 1, 1.05, 1.1, 1.15, 1.2, 1.25, 1.3), y1 = c(34, 30, 26, 23, 21, 19, 17, 16, 15, 13, 12, 12, 11), y2 = c(45, 39, 34, 31, 28, 25, 23, 21, 19, 17, 16, 15, 14)), .Names = c("x", "y1", "y2"), row.names = c(NA, -13L), class = "data.frame") library(reshape2); library(ggplot2) dat2 <- melt(dat, id='x') theme_minimal_cb_L <- function (base_size = 12, base_family = "", ...){ modifyList (theme_minimal (base_size = base_size, base_family = base_family), list (axis.line = element_line (colour = "black"))) } ggplot(data=dat2, aes(x=x, y=value, color=variable)) + geom_point(size=3) + geom_line(size=.5) + theme_minimal_cb_L()

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• R ggplot2: Arrange facet_grid by non-facet column (and labels using non-facet column)

  - by tommy-o-dell

  I have a couple of questions regarding facetting in ggplot2... Let's say I have a query that returns data that looks like this: (note that it's ordered by Rank asc, Alarm asc and two Alarms have a Rank of 3 because their Totals = 1798 for Week 4, and Rank is set according to Total for Week 4) Rank Week Alarm Total 1 1 BELTWEIGHER HIGH HIGH 1000 1 2 BELTWEIGHER HIGH HIGH 1050 1 3 BELTWEIGHER HIGH HIGH 900 1 4 BELTWEIGHER HIGH HIGH 1800 2 1 MICROWAVE LHS 200 2 2 MICROWAVE LHS 1200 2 3 MICROWAVE LHS 400 2 4 MICROWAVE LHS 1799 3 1 HI PRESS FILTER 2 CLOG SW 1250 3 2 HI PRESS FILTER 2 CLOG SW 1640 3 3 HI PRESS FILTER 2 CLOG SW 1000 3 4 HI PRESS FILTER 2 CLOG SW 1798 3 1 LOW PRESS FILTER 2 CLOG SW 800 3 2 LOW PRESS FILTER 2 CLOG SW 1200 3 3 LOW PRESS FILTER 2 CLOG SW 800 3 4 LOW PRESS FILTER 2 CLOG SW 1798 (duplication code below) Rank = c(rep(1,4),rep(2,4),rep(3,8)) Week = c(rep(1:4,4)) Total = c( 1000,1050,900,1800, 200,1200,400,1799, 1250,1640,1000,1798, 800,1200,800,1798) Alarm = c(rep("BELTWEIGHER HIGH HIGH",4), rep("MICROWAVE LHS",4), rep("HI PRESS FILTER 2 CLOG SW",4), rep("LOW PRESS FILTER 2 CLOG SW",4)) spark <- data.frame(Rank, Week, Alarm, Total) Now when I do this... s <- ggplot(spark, aes(Week, Total)) + opts( panel.background = theme_rect(size = 1, colour = "lightgray"), panel.grid.major = theme_blank(), panel.grid.minor = theme_blank(), axis.line = theme_blank(), axis.text.x = theme_blank(), axis.text.y = theme_blank(), axis.title.x = theme_blank(), axis.title.y = theme_blank(), axis.ticks = theme_blank(), strip.background = theme_blank(), strip.text.y = theme_text(size = 7, colour = "red", angle = 0) ) s + facet_grid(Alarm ~ .) + geom_line() I get this.... Notice that it's facetted according to Alarm and that the facets are arranged alphabetically. Two Questions: How can I can I keep it facetted by alarm but displayed in the correct order? (Rank asc, Alarm asc). Also, how can I keep it facetted by alarm but show labels from Rank instead of Alarm? Note that I can't just facet on Rank because ggplot2 would see only 3 facets to plot where there are really 4 different alarms. Thanks kindly for the help! Tommy

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• Show frequencies along with barplot in ggplot2

  - by aL3xa

  I'm trying to display frequencies within barplot ... well, I want them somewhere in the graph: under the bars, within bars, above bars or in the legend area. And I recall (I may be wrong) that it can be done in ggplot2. This is probably an easy one... at least it seems easy. Here's the code: p <- ggplot(mtcars) p + aes(factor(cyl)) + geom_bar() Is there any chance that I can get frequencies embedded in the graph?

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• ggplot2 heatmap : how to preserve the label order ?

  - by Tg

  I'm trying to plot heatmap in ggplot2 using csv data following casbon's solution in http://biostar.stackexchange.com/questions/921/how-to-draw-a-csv-data-file-as-a-heatmap-using-numpy-and-matplotlib the problem is x-label try to re-sort itself. For example, if I swap label COG0002 and COG0001 in that example data, the x-label still come out in sort order (cog0001, cog0002, cog0003.... cog0008). Is there anyway to prevent this ? I want to it to be ordered as in csv file thanks pp

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• Irrelevant legend information in ggplot2

  - by Dan Goldstein

  When running this code (go ahead, try it): library(ggplot2) (myDat <- data.frame(cbind(VarX=10:1, VarY=runif(10)), Descrip=sample(LETTERS[1:3], 10, replace=TRUE))) ggplot(myDat,aes(VarX,VarY,shape=Descrip,size=3)) + geom_point() ... the "size=3" statement does correctly set the point size. However it causes the legend to give birth to a little legend beneath it, entitled "3" and containing nothing but a big dot and the number 3. This does the same ggplot(myDat,aes(VarX,VarY,shape=Descrip)) + geom_point(aes(size=3)) Yes, it is funny. It would have driven me insane a couple hours ago if it weren't so funny. But now let's make it stop.

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• Error when trying to create a faceted plot in ggplot2

  - by John Horton

  I am trying to make a faceted plot in ggplot2 of the coefficients on the regressors from two linear models with the same predictors. The data frame I constructed is this: r.together> reg coef se y 1 (Intercept) 5.068608671 0.6990873 Labels 2 goodTRUE 0.310575129 0.5228815 Labels 3 indiaTRUE -1.196868662 0.5192330 Labels 4 moneyTRUE -0.586451273 0.6011257 Labels 5 maleTRUE -0.157618168 0.5332040 Labels 6 (Intercept) 4.225580743 0.6010509 Bonus 7 goodTRUE 1.272760149 0.4524954 Bonus 8 indiaTRUE -0.829588862 0.4492838 Bonus 9 moneyTRUE -0.003571476 0.5175601 Bonus 10 maleTRUE 0.977011737 0.4602726 Bonus The "y" column is a label for the model, reg are the regressors and coef and se are what you would think. I want to plot: g <- qplot(reg, coef, facets=.~y, data = r.together) + coord_flip() But when I try to display the plot, I get: > print(g) Error in names(df) <- output : 'names' attribute [2] must be the same length as the vector [1] What's strange is that qplot(reg, coef, colour=y, data = r.together) + coord_flip() plots as you would expect.

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• Placement of axis labels at minor breaks with ggplot2

  - by JAShapiro

  I am using ggplot2 to do some plotting of genomic data, so the basic format is that there is a chromosome and a position along it. I convert the positions to be on a continuous scale, then put the breaks at the boundaries of the chromosomes with: scale_x_continuous("Genome Position", breaks = c(0, cumsum(chromosome_length))) That looks great, as far as the actual plotting is concerned, but the labels are then put at the start and end of the chromosomes. I would like them to be centered along each chromosome, at the position where the minor break is drawn by default. Is this possible?

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• from ggplot2 to OOo workflow?

  - by Andreas

  This is not really a programming question, but I try here none the less. I once used latex for my reports. But the people I work with needs to make small edits and do not have latex skillz. Openoffice is then the way to go. But saving ggplot images with dpi 100 makes for really ugly graphs. dpi = 600 is a no go (e.g. huge legend). So what to do? I currently save (still via ggsave) to eps - which openoffice can import. But performance is not good at all. Googling I found a bug for the poor eps performance in OOo, and also talk about a non-implemented svg feature. But none helps me right now. If you work with ggplot2 and OOo - What do you do? I have been unsuccesfull with pdf conversion for some reason.

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• Side-by-side plots with ggplot2 in R

  - by chris_dubois

  I would like to place two plots side by side using the ggplot2 package (ie. do the equivalent of par(mfrow=c(1,2))). For example, I would like to have the following two plots show side-by-side with the same scale. x <- rnorm(100) eps <- rnorm(100,0,.2) qplot(x,3*x+eps) qplot(x,2*x+eps) Do I need to put them in the same data.frame like in this example? qplot(displ, hwy, data=mpg, facets = . ~ year) + geom_smooth() Thanks!

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• Adding trend lines/boxplots (by group) in ggplot2

  - by Tal Galili

  Hi all, I have 40 subjects, of two groups, over 15 weeks, with some measured variable (Y). I wish to have a plot where: x = time, y = T, lines are by subjects and colours by groups. I found it can be done like this: TIME <- paste("week",5:20) ID <- 1:40 GROUP <- sample(c("a","b"),length(ID), replace = T) group.id <- data.frame(GROUP, ID) a <- expand.grid(TIME, ID) colnames(a) <-c("TIME", "ID") group.id.time <- merge(a, group.id) Y <- rnorm(dim(group.id.time)[1], mean = ifelse(group.id.time$GROUP =="a",1,3) ) DATA <- cbind(group.id.time, Y) qplot(data = DATA, x=TIME, y=Y, group=ID, geom = c("line"),colour = GROUP) But now I wish to add to the plot something to show the difference between the two groups (for example, a trend line for each group, with some CI shadelines) - how can it be done? I remember once seeing the ggplot2 can (easily) do this with geom_smooth, but I am missing something about how to make it work. Also, I wondered at maybe having the lines be like a boxplot for each group (with a line for the different quantiles and fences and so on). But I imagine answering the first question would help me resolve the second. Thanks.

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• Smooth Error in qplot from ggplot2

  - by Jared

  I have some data that I am trying to plot faceted by its Type with a smooth (Loess, LM, whatever) superimposed. Generation code is below: testFrame <- data.frame(Time=sample(20:60,50,replace=T),Dollars=round(runif(50,0,6)),Type=sample(c("First","Second","Third","Fourth"),50,replace=T,prob=c(.33,.01,.33,.33))) I have no problem either making a faceted plot, or plotting the smooth, but I cannnot do both. The first three lines of code below work fine. The fourth line is where I have trouble: qplot(Time,Dollars,data=testFrame,colour=Type) qplot(Time,Dollars,data=testFrame,colour=Type) + geom_smooth() qplot(Time,Dollars,data=testFrame) + facet_wrap(~Type) qplot(Time,Dollars,data=testFrame) + facet_wrap(~Type) + geom_smooth() It gives the following error: Error in [<-.data.frame(*tmp*, var, value = list(NA = NULL)) : missing values are not allowed in subscripted assignments of data frames What am I missing to overlay a smooth in a faceted plot? I could have sworn I had done this before, possibly even with the same data.

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• jitter if multiple outliers in ggplot2 boxplot

  - by Andreas

  I am trying to find a suitable display to illustrate various properties within and across school classes. For each class there is only 15-30 data points (pupils). Right now i am leaning towards a whisker-less boxplot, showing only 1.,2. and 3. quartile + datapoints more then e.g. 1 population SD +/- the sample median. This I can do. However - I need to show this graph to some teachers, in order to gauge what they like most. I'd like to compare my graph with a normal boxplot. But the normal boxplot looks the same if there is only one outlier, or e.g. 5 outliers at the same value. In this case this would be a deal-breaker. e.g. test <-structure(list(value = c(3, 5, 3, 3, 6, 4, 5, 4, 6, 4, 6, 4, 4, 6, 5, 3, 3, 4, 4, 4, 3, 4, 4, 4, 3, 4, 5, 6, 6, 4, 3, 5, 4, 6, 5, 6, 4, 5, 5, 3, 4, 4, 6, 4, 4, 5, 5, 3, 4, 5, 8, 8, 8, 8, 9, 6, 6, 7, 6, 9), places = structure(c(1L, 2L, 1L, 1L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, 2L, 1L, 2L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 2L, 1L), .Label = c("a", "b"), class = "factor")), .Names = c("value", "places"), row.names = c(NA, -60L), class = "data.frame") ggplot(test, aes(x=places,y=value))+geom_boxplot() Here there are two outliers at ("a",9) - but only one "dot" shown. So my question: How to jitter the outliers. And - what kind of display would you suggest for this kind of data?

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• How do I increase the number of evaluation points in geom_smooth for ggplot2 in R

  - by Halpo

  I'm creating a plot and adding a basic loess smooth line to it. qplot(Age.GTS2004., X.d18O,data=deepsea, geom=c('point')) + geom_smooth(method="loess",se=T,span=0.01, alpha=.5, fill='light blue',color='navy') The problem is that the line is coming out really choppy. I need more evaluation point for the curve in certain areas. Is there a way to increase the number of evaluation points without having to reconstruct geom_smooth?

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• Transform only one axis to log10 scale with ggplot2

  - by daroczig

  I have the following problem: I would like to visualize a discrete and a continuous variable on a boxplot in which the latter has a few extreme high values. This makes the boxplot meaningless (the points and even the "body" of the chart is too small), that is why I would like to show this on a log10 scale. I am aware that I could leave out the extreme values from the visualization, but I am not intended to. Let's see a simple example with diamonds data: m <- ggplot(diamonds, aes(y = price, x = color)) The problem is not serious here, but I hope you could imagine why I would like to see the values at a log10 scale. Let's try it: m + geom_boxplot() + coord_trans(y = "log10") As you can see the y axis is log10 scaled and looks fine but there is a problem with the x axis, which makes the plot very strange. The problem do not occur with scale_log, but this is not an option for me, as I cannot use a custom formatter this way. E.g.: m + geom_boxplot() + scale_y_log10() My question: does anyone know a solution to plot the boxplot with log10 scale on y axis which labels could be freely formatted with a formatter function like in this thread? Editing the question to help answerers based on answers and comments: What I am really after: one log10 transformed axis (y) with not scientific labels. I would like to label it like dollar (formatter=dollar) or any custom format. If I try @hadley's suggestion I get the following warnings: > m + geom_boxplot() + scale_y_log10(formatter=dollar) Warning messages: 1: In max(x) : no non-missing arguments to max; returning -Inf 2: In max(x) : no non-missing arguments to max; returning -Inf 3: In max(x) : no non-missing arguments to max; returning -Inf With an unchanged y axis labels:

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• Can ggplot2 work with R's canvas backend

  - by Casbon

  Having installed canvas from here http://www.rforge.net/canvas/files/ I try to plot: > canvas('test.js') > qplot(rnorm(100), geom='histogram') stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' to adjust this. Error in grid.Call.graphics("L_setviewport", pvp, TRUE) : Non-finite location and/or size for viewport >

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