wilkelab/cowplot

cowplot: Streamlined Plot Theme and Plot Annotations for ggplot2

cowplot's Issues

Shared Common Legend Between Panels

Hi,

I was just wondering if you had a method/technique to have a common legend across multiple plots using the cowplot library? This is similar to the idea listed here:

https://github.com/hadley/ggplot2/wiki/Share-a-legend-between-two-ggplot2-graphs

Thanks,

Fong

Labels do not align correctly in 12 panel figure using Cowplot - plot_grid

I used plot_grid to generate a 12 (3 row by 4 col) panel figure, however, I was not able to get the alignment correct for the 3rd row after "hjust = -6".
Thank you for your time and help!

PP1 <- ggplot(mpg, aes(x = cty, y = hwy, colour = factor(cyl))) + geom_point(size = 2.5)
....

PP12 <- ggplot(mpg, aes(x = cty, y = hwy, colour = factor(cyl))) + geom_point(size = 2.5)

plot3by4 <- plot_grid(PP1, PP2, PP3, PP4, PP5, PP6, PP7, PP8, PP9, PP10, PP11, PP12, labels=c("A", "B", "C", "D","E", "F", "G", "H", "I", "J", "K", "L"), ncol = 4, nrow = 3, align = 'v', hjust=-6, label_size=17)

save_plot("plot3by4.png", plot3by4, ncol = 4, nrow = 3, base_aspect_ratio = 1 )

using knitr, cowplot not printing if a plot exists in the RSTUDIO GUI

Hi,
I am using RSTUDIO and knitr. I use cowplot to put graphs in a custom grid. If a plot is present in the RSTUDIO UI, then not plot shows in the produced pdf. If I erase the plots (effectively using dev.off()) then the plots are now knitted.
Doing the grid manually, using grid, does not have the same issue. I like cowplot's clarity though. good job

Is this is related to #24?

Thanks

sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                            LC_TIME=English_United Kingdom.1252    

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] ggrepel_0.6.3   plotly_4.5.6    cowplot_0.7.0   shiny_0.14.2    xtable_1.8-2    readxl_0.1.1    tidyr_0.6.0     stringr_1.1.0   dplyr_0.5.0    
[10] lubridate_1.6.0 gridExtra_2.2.1 reshape2_1.4.2  scales_0.4.1    ggplot2_2.2.0   knitr_1.15     

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.7        magrittr_1.5       munsell_0.4.3      viridisLite_0.1.3  colorspace_1.3-0   R6_2.2.0           httr_1.2.1        
 [8] plyr_1.8.4         tools_3.3.2        gtable_0.2.0       DBI_0.5-1          htmltools_0.3.5    lazyeval_0.2.0     assertthat_0.1    
[15] digest_0.6.10      tibble_1.2         purrr_0.2.2        RColorBrewer_1.1-2 htmlwidgets_0.8    base64enc_0.1-3    evaluate_0.10     
[22] mime_0.5           labeling_0.3       stringi_1.1.2      jsonlite_1.1       httpuv_1.3.3      

Set strip background to white

A (very) minor suggestion to set the strip background colour to white as default. I love the clean overall look of the cowplot theme, but always end up manually changing the grey strip background whenever I am using cowplot with a faceted or gridded plot:

theme(strip.background = element_rect(fill = "white"))

Hardly a game changer, but I do think it better suits the general ethos of the theme.

Allow adding vanilla R plots to plot_grid

some plotting functions use normal plotting instead of grid-based plotting.

it would be useful to be able to pass recordedPlot instances or functions that draw on the R device to plot_grid.

currently I use this function, which could be added to cowplot internally:

gwrap_plot <- function(x) {
    tree <- grid::grid.grabExpr(gridGraphics::grid.echo(x))
    u <- grid::unit(1, 'null')
    gtable::gtable_col(NULL, list(tree), u, u)
}

gridGraphics::grid.echo accepts either a function like function() plot(1:10) or a recordedPlot object, and we could do the same.

This would lead to neat code like this:

p1 <- ggplot(...) + ...
p2 <- function() plot(1:10)

plot_grid(p1, p2)

an alternative would be to stay explicit, but export above function (with a better name than gwrap_plot)

The Vignette title metadata needs editing

The vignette currently has

%\VignetteIndexEntry{Vignette Title} 

Which should be edited to be an appropriate and relevant title for the vignette. Currently CRAN displays the vignette with the name "Vignette Title".

switch_axis_position error with axis.title.y=element_blank()

Paste this message in R console to reproduce the error

An error occurs on switching the y-axis (but not on the x-axis) when removing axis titles

p1 <- ggplot(mtcars, aes(mpg, disp)) + geom_line(colour = "blue")+
theme(axis.title.x=element_blank(),axis.title.y=element_blank())
ggdraw(switch_axis_position(p1, axis = 'x'))

No problem

p1 <- ggplot(mtcars, aes(mpg, disp)) + geom_line(colour = "blue")+
theme(axis.title.x=element_blank(),axis.title.y=element_blank())
ggdraw(switch_axis_position(p1, axis = 'y'))

This doesn't work, and i get the following error message

Error in Ops.unit(gyl$x, grid::unit(0.5, "npc")) : both operands must be units

The same error occurs on 'xy'. Any ideas?

Align X axis

Below code illustrates the problem. When 2 plots merged using plot_grid, is it possible to make X axis to align. i.e.: xlims are derived from 2 plots.

library(ggplot2)
library(cowplot)

df1 <- iris
df2 <- iris

df2 <- df2[df2$Sepal.Length <6, ]
df2$Sepal.Width <- df2$Sepal.Width*10000

#ggplot
gg1 <- ggplot(df1, aes(x=Sepal.Length, y=Sepal.Width, color=Species)) + geom_line()
gg2 <- ggplot(df2, aes(x=Sepal.Length, y=Sepal.Width, color=Species)) + geom_line()

#merge
plot_grid(gg1, gg2, labels = c("A", "B"), align = "v",ncol = 1)

install.packages not working for me

When I try install.packages("cowplot") on my Mac, I get this response:

package ‘cowplot’ is available as a source package but not as a binary
Warning in install.packages :
package ‘cowplot’ is not available (for R version 3.1.2)

Installing from GitHub works fine.

plot_grid() interaction with theme_set()

Hi there,

thanks for this useful package. Since one of the more recent updates (before updating to the current version I used 0.6.2) I'm experiencing some weird issues with the interaction between plot_grid(), theme_set(), and a theme of mine that modifies axis.text.x.

Everything works great as long as I don't use theme_set().

Works as expected:

library("ggplot2")
library("cowplot")

df <- data.frame(
  gp = factor(rep(letters[1:3], each = 10)),
  y = rnorm(30)
)

test <- ggplot(df, aes(gp, y)) +
  geom_point() +
  theme_classic() + 
  theme(axis.text.x = element_text())

plot_grid(test)

Throws an error:

theme_set(theme_classic() + theme(axis.text.x = element_text()))

test2 <- ggplot(df, aes(gp, y)) +
  geom_point()

plot_grid(test2)

Error in element_grob.element_text(el, ...) : 
  Text element requires non-NULL value for 'angle'.

If I set angle I get another error:

theme_set(theme_classic() + theme(axis.text.x = element_text(angle = 0)))

plot_grid(test2)

Error in if (debug) { : Argument has length 0

Now, if I set debug = FALSE it finally works, but I get some weird numbering on the bottom margin.

This is my session info:

Session info ---------------------------------------------------------------------------------------------------------------------------
 setting  value                       
 version  R version 3.3.2 (2016-10-31)
 system   x86_64, linux-gnu           
 ui       RStudio (1.0.136)           
 language de_DE                       
 collate  de_DE.UTF-8                 
 tz       <NA>                        
 date     2017-02-24                  

Packages -------------------------------------------------------------------------------------------------------------------------------
 package    * version  date       source                           
 assertthat   0.1      2013-12-06 CRAN (R 3.3.0)                   
 colorspace   1.2-6    2015-03-11 CRAN (R 3.3.0)                   
 cowplot    * 0.7.0    2017-02-24 Github (wilkelab/cowplot@78336ac)
 devtools     1.12.0   2016-06-24 CRAN (R 3.3.1)                   
 digest       0.6.11   2017-01-03 CRAN (R 3.3.2)                   
 ggplot2    * 2.2.1    2016-12-30 CRAN (R 3.3.2)                   
 gtable       0.2.0    2016-02-26 CRAN (R 3.3.0)                   
 labeling     0.3      2014-08-23 CRAN (R 3.3.0)                   
 lazyeval     0.2.0    2016-06-12 CRAN (R 3.3.0)                   
 memoise      1.0.0    2016-01-29 CRAN (R 3.3.0)                   
 munsell      0.4.3    2016-02-13 CRAN (R 3.3.0)                   
 plyr         1.8.4    2016-06-08 CRAN (R 3.3.0)                   
 Rcpp         0.12.9.3 2017-02-24 Github (RcppCore/Rcpp@8bf15c0)   
 scales       0.4.1    2016-11-09 CRAN (R 3.3.2)                   
 tibble       1.2      2016-08-26 CRAN (R 3.3.1)                   
 withr        1.0.2    2016-06-20 CRAN (R 3.3.1)

Main Title for Plots

I realize cowplot is publication-focused,and this isn't usually something you see in publications, but it would be useful if there was a "main title" attribute you could set describing what the plots are. This would just be centered text above all the plots

Tiny agreement error in vignette

"there are important but subtle difference" --> differences.

Using switch_axis_position() with facet_grid()

I would like to switch the position of the y axis to the right hand side of my plot using

ggdraw(switch_axis_position(p1, axis = 'y'))

However, my plot is facetted using facet_grid, and so I get the error "Error in switch_yaxis_position(gt, theme, keep.y): Can only switch axes on plots with exactly one panel."

Is there any way to work around this? Just for clarification, I'd like my y axis to be on the far right hand side of my facetted plot.. Thank you!

finer control of alignment

Thanks for cowplot. It's really been a game changer for making publication quality plots in R.

Would it be possible to implement finer control for subplot alignment in plot_grid? For example, I have a grid like the following

XXXXXXXX XX
XXXXXXXX XX
XXXXXXXX XX

I would like to separately horizontally align the plots in the left column, horizontally align the plots in the left column, and vertically align the plots in each row.

When I use align = 'hv', the end result is that everything has both the same height and width, which is not what I'd like.

Thanks.

Errors loading cowplot

Trying to load cowplot fails on R 3.2.3.

Both commands
install.packages("cowplot")
and
devtools::install_github("wilkelab/cowplot")
compile fine.

Upon loading with require(cowplot) I get the following error:
Loading required package: cowplot
Error : .onAttach failed in attachNamespace() for 'cowplot', details:
call: element_text(family = font_family, face = "plain", colour = "black",
error: unused arguments (margin = ggplot2::margin(), debug = FALSE)

Can't install cowplot in RStudio R 3.2.0?

Attempt to install in RStudio Version 0.99.441 Win 8.1

> install.packages("cowplot")
Warning in install.packages :
  package ‘cowplot’ is not available (for R version 3.2.0)

May be lag in CRAN.

plot arrangement powered by `gtable`

Thanks really for this great packages.
I have one suggestion.

ggplot2 uses gtable as its backend structure for grid-based plot generation.
gtable allows to arrange multiple plots keeping their panel sizes aligned.

Here are some examples, sorry for Japanese text, but the codes are easy to read :)
http://rpubs.com/kohske/84415

So, it is really excellent if cowplot support this kind of arrangement powered by gtable.
Then we can get grid plots with consistent size for all panes and axes.

Feel free please to ask anything, if you have any question regarding usage of gtable, as I'm one of the committer of the package.

Thanks again.

-k

Can't remove axis text and ticks when switching axis position

I had the following error
Error in Ops.unit(grid::unit(1, "npc"), grob$children[[1]]$y) :
both operands must be units

Code I used:

mtcars2 <- mtcars[1:15, ]
mtcars2$name <- row.names(mtcars2)
p3 <- ggplot(mtcars2, aes(x = name, y = mpg, fill = name)) +
geom_bar(stat = 'identity', position = "identity") +
scale_y_reverse() +
guides(fill = FALSE) +
theme(axis.text.x = element_blank(), axis.ticks.x = element_blank())
ggdraw(switch_axis_position(p3, axis = 'x'))

Any idea what went wrong? Thanks!

Tung

Increasing the space between plots in plot_grid?

Is it possible to increase the spacing between the plots in plot_grid?

The spacing I found discussed in the docs all seemed to refer to labels within plots.

cowplot axis rotation

Unable to justify legend when combining plots with plot_grid()

I am using data sourced from the PDF on this page. Specifically: table 4 on page 14. You can see that there are three categories of data in this table, which I am trying to combine in a single plot. However, the legend text has different lengths which causes the legends to look ugly - because they are all centred and it does not seem to be possible to change this. I have try to left-justify the legend using legend.justification = c(0,0) in my call to ggplot() but this appears to be overriden by plot_grid().

Vertical alignment not working for switched axes

This package is fantastic! I like the switch axis functionality but would like to be able to combine it with vertical grid alignment and it doesn't seem to work:

plot.mpg1 <- ggplot(mpg, aes(x = cty, y = hwy, colour = factor(cyl))) + 
  geom_point(size=2.5)
plot.mpg2 <- ggplot(mpg, aes(x = cty, y = hwy, colour = factor(cyl))) + 
  geom_point(size=2.5)

plot.mpg2 <- switch_axis_position(plot.mpg2, "y")
plot_grid(plot.mpg1, plot.mpg2, nrow = 2, align = "v")

Shrink y axis title margins

Hi there,

Big fan of cowplot - thanks for putting it out there. Wondering if there's a way to squish the y axis title margins when needed? In the attached figure, one can see that too much space is being allocated for the titles (sorry, obligated to obfuscate the words themselves, but i think it's good enough to understand the issue). I've tried setting theme(y.axis.title(margin = margin(0,0,0,0)) when constructing the constitutent plots, but it has no effect on cowplot's output. Any help would be greatly appreciated!

Thanks,
Alex

Workaround ggplot2 2.1.0 and axis lines not shown

I have just realised that ggplot2 are not plotting axis lines by default (tidyverse/ggplot2#1565 and tidyverse/ggplot2#1567). I imagine this is a mistake, and a work around for now is to issue

theme_set(theme_cowplot() + theme(axis.line.x = element_line(), axis.line.y = element_line()))

after loading the cowplot library.

The problem seems to be just with ggplot2 2.1.0

Side effect from merely loading the package

I've noticed that by simply loading the package, the ggplot2 theme is changed

https://github.com/wilkelab/cowplot/blob/master/R/setup.R#L5-L8

I feel like this is not a good practice, and it's a bit annoying and unpredictable. Would be nice if there was an explicit way to revert back, and even better if attaching the package would not have this side effect.

Stop enforcing to use specific theme

Whenever I tried to use cowplot, it changes my theme which is devastating, since a lot of effort was given to get the appearances.

plot_grid and theme_update(panel.grid.major)

In general, I really like the minimalistic theme settings of cowplot. However, I also like having the major grid, and I find it easier to set it up globally at the beginning of my scripts. It works fine for single plots, but seems to confuse plot_grid, which plots a grid on top of the grid plot (and not only on top of single plots).

Here is a better explanation with simple iris plots:

library(cowplot)
i1 <- ggplot(iris, aes(Sepal.Length, Sepal.Width)) +
    geom_point()
i2 <- ggplot(iris, aes(Petal.Length, Petal.Width)) +
    geom_point()
i3 <- ggplot(iris, aes(Sepal.Length, Petal.Length)) +
    geom_point()
i4 <- ggplot(iris, aes(Sepal.Width, Petal.Width)) +
    geom_point()
plot_grid(i1, i2, i3, i4)

This works perfectly. I can use background_grid to add the grid manually to each plot:

i1 <- ggplot(iris, aes(Sepal.Length, Sepal.Width)) +
    geom_point() + background_grid(major = 'xy')
i2 <- ggplot(iris, aes(Petal.Length, Petal.Width)) +
    geom_point() + background_grid(major = 'xy')
i3 <- ggplot(iris, aes(Sepal.Length, Petal.Length)) +
    geom_point() + background_grid(major = 'xy')
i4 <- ggplot(iris, aes(Sepal.Width, Petal.Width)) +
    geom_point() + background_grid(major = 'xy')
plot_grid(i1, i2, i3, i4)

Still works as expected. Now if I update the theme to add the major grid to all plots:

theme_update(panel.grid.major = element_line(colour = "grey90",
    size = 0.2))
i1 <- ggplot(iris, aes(Sepal.Length, Sepal.Width)) +
    geom_point()
i2 <- ggplot(iris, aes(Petal.Length, Petal.Width)) +
    geom_point()
i3 <- ggplot(iris, aes(Sepal.Length, Petal.Length)) +
    geom_point()
i4 <- ggplot(iris, aes(Sepal.Width, Petal.Width)) +
    geom_point()
plot_grid(i1, i2, i3, i4)

I get the additional grid on top of the combined plot. I didn't attach a picture of it, so please let me know if it's only happening on my computer (note: using Debian Testing, with R 3.3.2, ggplot 2.2.1 and cowplot 0.7.0).

Thanks for looking at this issue!

save_plot: dimensions not computed as documented?

Hello there,
I followed https://cran.r-project.org/web/packages/cowplot/cowplot.pdf
to create some plotgrids files.

However, in the pdf or svg files I get the dimensions do not seem to be computed based on definitions for the "base plot" size or ratios. (This is what the documentation suggested to me, and looked very practical to me.)

It looks like the definitions are applied to the final entire plotgrid.

In the following example:

• I only get the two side-by-side plots with a proper 45 degree slope when the ratio is adjusted according to the grid dimensions (set to 2).
• I only get two stacked plots with a proper 45 degree slope with a ratio of 0.5, however the graphics look crammed.

require(dplyr)
require(ggplot2)
require(cowplot)

tmp_plot1 <- data.frame(a=1:100, b=1:100) %>%
  ggplot(aes(x=a, y=b)) + geom_line()

tmp_plot2 <- tmp_plot1

tmp_plotgrid <- plot_grid(tmp_plot1, tmp_plot2, labels = c('A', 'B'))

save_plot("2-horizontal-plots_height-NA_aspect-1.pdf", tmp_plotgrid, base_aspect_ratio = 1)
save_plot("2-horizontal-plots_height-NA_aspect-2.pdf", tmp_plotgrid, base_aspect_ratio = 2)
save_plot("2-horizontal-plots_height-NA_aspect-3.pdf", tmp_plotgrid, base_aspect_ratio = 3)

tmp_plotgrid <- plot_grid(tmp_plot1, tmp_plot2, labels = c('A', 'B'), ncol = 1)

save_plot("2-vertical-plots_height-NA_aspect-0.5.pdf", tmp_plotgrid, base_aspect_ratio = 0.5)
save_plot("2-vertical-plots_height-NA_aspect-1.pdf", tmp_plotgrid, base_aspect_ratio = 1)
save_plot("2-vertical-plots_height-NA_aspect-2.pdf", tmp_plotgrid, base_aspect_ratio = 2)
save_plot("2-vertical-plots_height-NA_aspect-3.pdf", tmp_plotgrid, base_aspect_ratio = 3)

Decreasing the space between plots in plot_grid?

I've tried the reverse of the solutions suggested in #11, and the plots end up with parts cut off. Thanks in advance!

Axis label justification goes bananas after `switch_axis_position` for `angle = 90`

While answering a question on stackoverflow I found that the justification for the axis labels seems to bug out if the angle is 90 degrees.

A simple (hackish) fix is to add a small amount to the degrees.

Example:

library(reshape2)
library(ggplot2)
library(cowplot)

# some toy data
set.seed(1)
mydata <- mtcars[, c(1, 3, 4, 5, 6, 7)]

# to show difference in justification better, make names of unequal length 
names(mydata) = paste0(sample(c("mtcars_", ""), 6, replace = TRUE), names(mydata))
cormat <- round(cor(mydata), 2)

melted_cormat <- melt(cormat)
head(melted_cormat)


plot <- ggplot(data = melted_cormat, aes(x=Var1, y=Var2, fill=value)) + 
        geom_tile() +
        theme_bw(base_size=20) + xlab("") + ylab("") +
        theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 0.5))
ggdraw(switch_axis_position(plot, 'x'))

This gives weird labels (you can mess around with vjust and hjust).

But this version gives the desired result:

plot <- ggplot(data = melted_cormat, aes(x=Var1, y=Var2, fill=value)) + 
  geom_tile() + theme_bw(base_size=20) + xlab("") + ylab("")+
  theme(axis.text.x=element_text(angle=90 + 1e-09, hjust = 0, vjust=1)) +
  coord_equal(expand = 0)
ggdraw(switch_axis_position(plot, 'x'))

Thanks for a great package!

Warning when plot via plot_grid whith French Accent

Hello
When I run this code :
ggplot(data.frame(a=1:5, b = 1:5), aes(a,b)) + geom_point() + labs(title = "é")

No problem
But this one make a Warning :
toto<- ggplot(data.frame(a=1:5, b = 1:5), aes(a,b)) + geom_point() + labs(title = "é")
plot_grid(toto)

Why ?
I use this in a knitr file and can not ignore them
Thank you for any help

regression: unintuitive behavior with modifying cowplot theme

I quite like the cowplot theme, but I ran into a problem modifying the theme to remove both axis.text.y and .x using theme(axis.text = element_blank()).

library(ggplot2)
ggplot(mtcars, aes(wt, mpg)) + geom_point() + theme(axis.text = element_blank())
library(cowplot)
#> Warning: `legend.margin` must be specified using `margin()`. For the old
#> behavior use legend.spacing
#> 
#> Attaching package: 'cowplot'
#> The following object is masked from 'package:ggplot2':
#> 
#>     ggsave
ggplot(mtcars, aes(wt, mpg)) + geom_point() + theme(axis.text = element_blank())
#> Error in element_grob.element_text(el, ...) : 
#>  Text element requires non-NULL value for 'angle'.

This worked at one point, but unfortunately I don't know the version numbers when it did (sometime around the end of July, if that helps). The work around is to specify both axis.text.y and axis.text.x directly.

devtools::session_info()
#> Session info -------------------------------------------------------------
#>  setting  value                       
#>  version  R version 3.3.1 (2016-06-21)
#>  system   x86_64, darwin13.4.0        
#>  ui       X11                         
#>  language (EN)                        
#>  collate  en_US.UTF-8                 
#>  tz       America/New_York            
#>  date     2016-11-04
#> Packages -----------------------------------------------------------------
#>  package    * version     date       source                          
#>  assertthat   0.1         2013-12-06 CRAN (R 3.3.0)                  
#>  clipr        0.2.1       2016-06-23 cran (@0.2.1)                   
#>  colorspace   1.2-6       2015-03-11 CRAN (R 3.3.0)                  
#>  cowplot    * 0.6.2       2016-04-20 CRAN (R 3.3.0)                  
#>  curl         2.1         2016-09-22 cran (@2.1)                     
#>  devtools     1.12.0.9000 2016-10-27 Github (hadley/devtools@f0d1c7e)
#>  digest       0.6.10      2016-08-02 cran (@0.6.10)                  
#>  evaluate     0.10        2016-10-11 cran (@0.10)                    
#>  formatR      1.4         2016-05-09 CRAN (R 3.3.0)                  
#>  ggplot2    * 2.1.0.9001  2016-11-03 Github (hadley/ggplot2@9869339) 
#>  git2r        0.15.0      2016-05-11 CRAN (R 3.3.0)                  
#>  gtable       0.2.0       2016-02-26 CRAN (R 3.3.0)                  
#>  htmltools    0.3.5       2016-03-21 CRAN (R 3.3.0)                  
#>  httr         1.2.1       2016-07-03 cran (@1.2.1)                   
#>  knitr        1.14        2016-08-13 cran (@1.14)                    
#>  lazyeval     0.2.0       2016-06-12 CRAN (R 3.3.0)                  
#>  magrittr     1.5         2014-11-22 CRAN (R 3.3.0)                  
#>  memoise      1.0.0       2016-01-29 CRAN (R 3.3.0)                  
#>  munsell      0.4.3       2016-02-13 CRAN (R 3.3.0)                  
#>  plyr         1.8.4       2016-06-08 CRAN (R 3.3.0)                  
#>  R6           2.2.0       2016-10-05 cran (@2.2.0)                   
#>  Rcpp         0.12.7      2016-09-05 cran (@0.12.7)                  
#>  reprex       0.0.0.9001  2016-11-04 Github (jennybc/reprex@826ddf4) 
#>  rmarkdown    1.1         2016-10-16 cran (@1.1)                     
#>  scales       0.4.0.9003  2016-11-03 Github (hadley/scales@d58d83a)  
#>  stringi      1.1.1       2016-05-27 CRAN (R 3.3.0)                  
#>  stringr      1.1.0       2016-08-19 cran (@1.1.0)                   
#>  tibble       1.2         2016-08-26 cran (@1.2)                     
#>  withr        1.0.2       2016-06-20 cran (@1.0.2)

Why is R 3.2 needed?

I just tried to use cowplot::plot_grid with a fork of this repo, changing the minimum version of R to 3.1.2. It worked. Admittedly, I did not try all the functions of cowplot, but it worked enough for my case, and I avoided upgrading R to 3.2, which might break some other things. So I was just wondering, is the 3.2 version really necessary, or is it possible to relax this requirement so that older versions might profit from this package?

Cheers

plot_grid: avoid squishing due to axis label

Hi there,

I asked this on stackoverflow (http://stackoverflow.com/questions/39530116/arrange-multiple-ggplots-but-avoid-squishing-due-to-axis-label/39532814), but wasn't able to resolve it, so am coming here.

I've been using cowplot::plot_grid to arrange multiple ggplot figures, which has been working great in general. However, I've now run into a problem where I want to include the x axis labels on just the bottom plot, but it ends up squishing all the plots (with align = "vh") or the lowest plot (with align = "v") in the column.

Is there any way to perhaps extract the x-axis label grob, and add that as a another plot in plot_grid (perhaps similar to https://github.com/wilkelab/cowplot/blob/master/vignettes/shared_legends.Rmd for legends)? Or another approach?

Thanks very much!

library(ggplot2)
library(cowplot)

a = data.frame(a = rnorm(100), b = rep(c("laskjdflsakjd", "cknmlokfjoweijojf"), 50))
b = data.frame(a = rnorm(100), b = rep(c("laskjdflsakjd", "cknmlokfjoweijojf"), 50))
c = data.frame(a = rnorm(100), b = rep(c("laskjdflsakjd", "cknmlokfjoweijojf"), 50))

aplot = ggplot(a, aes(x=b, y=a)) + geom_bar(stat = "identity")
bplot = ggplot(b, aes(x=b, y=a)) + geom_bar(stat = "identity")
cplot = ggplot(c, aes(x=b, y=a)) + geom_bar(stat = "identity") + theme(axis.text.x = element_text(angle=90, vjust = 0.5))

plot_grid(aplot + theme(axis.text.x = element_blank(), axis.title.x = element_blank()),
        bplot + theme(axis.text.x = element_blank(), axis.title.x = element_blank()),
        cplot, ncol = 1, align = "vh")

Unable to change the color of axis.line

I've just started to use ggplot2 and cowplot so I might be wrong.

For some reason the color of the axis.line element cannot be changed.
I can change the color of other elements, even axis.ticks.

Add an plot_label option to plot_grid()

I personally prefer (and I believe some journals demand) that the figure number is printed on the figure. My reason is that it creates less confusion when figures are bundled into one pdf or printed. It is possible to do this now but only by combinations of ggdraw(), draw_plot, and draw_label().

I suggest that the argument plot_label = NULL is added to the plot_grid(), the addition to the function body could be

if(!isnull(plot_label)){
  p <- p + draw_label(plot_label, 1, 0, hjust = 1, vjust = 0)
}

The x, y, hjust, and vjust could also be given as arguments to the function, but I think that would be too much.

Using align='hv' in plot_grid ignores defined margins

I'm having an issue trying to reduce the margins around my plots in plot_grid.

Using align='hv' perfectly aligns and scales my axes but leaves unwanted whitespace between plots, like so:

Whereas defining margins within each plot reduces the whitespace as desired, but leaves the y axes misaligned due to their different sizes, like so:

I've included a reproducible example below.

Thanks in advance for any help on this matter -- I appreciate the work you're doing with cowplot.

#my data
mydat <- structure(list(sex = structure(c(2L, 2L, 2L, 2L, 2L, 2L, 1L, 
1L, 1L, 1L, 1L, 1L), .Label = c("F", "M"), class = "factor"), 
    treat = structure(c(3L, 3L, 1L, 1L, 2L, 2L, 3L, 3L, 1L, 1L, 
    2L, 2L), .Label = c("nylon", "stab", "no treat"), class = "factor"), 
    pre_post = structure(c(2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 
    1L, 2L, 1L), .Label = c("pre", "post"), class = "factor"), 
    meanPO = c(0.271111104444444, 2.32355555333333, 0.288222211111111, 
    0.15, 0.254444435555555, 1.86595237619048, 0.164901954901961, 
    0.247333333333333, 0.794901970588235, 0.6429166625, 0.390196078431373, 
    0.339777768888889), meanproPO = c(1.17066665333333, 3.96755554888889, 
    1.68466666666667, 0.750888877777778, 1.11022221777778, 2.90190476428571, 
    0.269411770588235, 0.493777764444444, 0.790392158823529, 
    0.926458333333333, 0.529583329166667, 0.803111106666667)), .Names = c("sex", 
"treat", "pre_post", "meanPO", "meanproPO"), class = "data.frame", row.names = c(13L, 
15L, 17L, 19L, 21L, 23L, 1L, 3L, 5L, 7L, 9L, 11L))

#individual plots

#set common themes
my_theme <- theme(
    legend.position="none",
    axis.line = element_line(colour = "black")
)
#plot 1
gg_TL <- ggplot(subset(mydat, sex=="F"), aes(x=treat, y=meanPO, fill=pre_post)) +
    geom_bar(position="dodge", stat="identity", width=0.75) +
    scale_y_continuous(limits=c(0,my_ylim), expand=c(0,0) ) +
    labs(x="") +
    my_theme + theme(
        axis.text.x = element_blank()
    )
#plot 2
gg_BL <- ggplot(subset(mydat, sex=="F"), aes(x=treat, y=meanproPO, fill=pre_post)) +
    geom_bar(position="dodge", stat="identity", width=0.75) +
    scale_y_continuous(limits=c(0,my_ylim), expand=c(0,0) ) +
    labs(x="") +
    my_theme
#plot 3
gg_TR <- ggplot(subset(mydat, sex=="M"), aes(x=treat, y=meanPO, fill=pre_post)) +
    geom_bar(position="dodge", stat="identity", width=0.75) +
    scale_y_continuous(limits=c(0,my_ylim), expand=c(0,0) ) +
    labs(x="", y="") +
    my_theme + theme(
        axis.text.x = element_blank()
    )
#plot 4
gg_BR <- ggplot(subset(mydat, sex=="M"), aes(x=treat, y=meanproPO, fill=pre_post)) +
    geom_bar(position="dodge", stat="identity", width=0.75) +
    scale_y_continuous(limits=c(0,my_ylim), expand=c(0,0) ) +
    labs(y="", x="") +
    my_theme

# cowplot
# Plot #1: hv align
plot_grid(gg_TL, gg_TR, gg_BL, gg_BR, labels = LETTERS[1:4], label_size = 18, align="hv")

# Plot #2: define margins of each plot, no hv align
gg_TL <- gg_TL + theme(plot.margin=unit(c(0.6,-0.2,-0.5,0.2), "cm")) 
gg_BL <- gg_BL + theme(plot.margin=unit(c(0.6,-0.2,-0.5,0.2), "cm"))
gg_TR <- gg_TR + theme(plot.margin=unit(c(0.4,0.2,-0.5,0.2), "cm"))
gg_BR <- gg_BR + theme(plot.margin=unit(c(0.4,0.2,-0.5,0.2), "cm"))
plot_grid(gg_TL, gg_TR, gg_BL, gg_BR, labels = LETTERS[1:4], label_size = 18)

Suggestion: better facet grid separation

I like the defaults set by the package, plot look much more publication-ready. I have a small change which you could add to a vignette if setting it globally would hurt:

theme_update(panel.margin = grid::unit(0.05,"lines"))

Without this, faceted graphs look confusing.

R version requirement

I was wondering if there is a functional reason for this version to require R 3.2. I manually installed it on my R 3.1.2 and all functions I tried seems to be compatible. No errors on installation and past scripts work without issues. Is there a test suite that I could run if information isn't available on this?

cowplot not available issue - R 3.2.3

Hey,

I run into the (much-reported) issue "package ‘cowplot’ is not available (for R version 3.2.3)" when I run install.packages("cowplot", repos="http://cran.r-project.org/") on my Windows 10 machine.
Can you help solve this?

Thanks, best
Jana

Font for labels for plot_grid

Hi everyone

I've just started to use ggplot2 and cowplot so I might be overlooking something. I've set the font family for cowplot to helvetica, but it seems that the large figure labels for cowplot are still arial. (shown in the attached file, there is a difference between the G of the X axis and the large label for the actual figure) There doesn't seem to be an option to change the font under plot grid.

Relevant code:

theme_set(theme_cowplot(font_size=12,font_family = "helvetica")) 
plot_grid(g.fwd, g.rev, labels = c('G', 'B'), ncol=1)

Add common title for the grouped plot and place each label inside individual plots?

I'm wondering if it's possible to add a common main title for grouped plot? Also is there an option to place each label (e.g. "A", "B") inside individual plots

Thanks!

Zoom functionality

See below issue for ggforce package:

thomasp85/ggforce#59

Could we have an argument showZoom = TRUE and show the shading on how vertically aligned plots related through xaxis?

error in using 'cowplot' package

I have some issues with 'cowplot', I guess, compatability with 'qqplot2'
When I 'cowplot' package uploaded, I constantly get an error for every plot that I try to run:
Error in FUN("text"[[1L]], ...) : Theme element 'text' has NULL property: margin, debug
I have read some recommendations about this issue to add
margin =margin(), debug=F
so I added it as following:
element_text(size=14, vjust=2, face="bold", margin =margin(), debug=F)
but it did not help.
This is very weird, because 2 weeks ago everything worked perfectly fine, but yesterday and today whenever I download 'cowplot', I get this errors for all the plots, disregarding of whether I use 'cowplot' function or not.

Default subplot label in plot_grid()

The plot_grid() is a great way of making plots ready for publication. However, I think it would make sense if the subplots are labelled with upper-case letters by default.

The option labels = NULL in plot_grid() could be changed labels = "auto" and by adding

if("auto" %in% labels){
  labels <- LETTERS[1:num_plots]
}

to the body of the function, the subplot labels will be generated automatically.

The num_plots is already used in the function.

Unexpected blank page in pdf

When I run the following I get an unexpected blank page when I save to pdf. Include the theme(legend.position = "none") or save via ggsave() everything is fine.

library(cowplot)

plot.df <- data.frame(value = rnorm(10), variable = c("A", "B"))

p <- ggplot(plot.df, aes(x = variable, y = value, fill = variable))
p <- p + geom_boxplot()

pdf(file = "with_legend.pdf")
plot_grid(p)
dev.off()

pdf(file = "without_legend.pdf")
plot_grid(p + theme(legend.position = "none"))
dev.off()

p
ggsave(filename = "by_gsave.pdf")

My sessionInfo()

R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 15.10

locale:
 [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C               LC_TIME=de_DE.UTF-8        LC_COLLATE=de_DE.UTF-8     LC_MONETARY=de_DE.UTF-8   
 [6] LC_MESSAGES=de_DE.UTF-8    LC_PAPER=de_DE.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] cowplot_0.6.0 ggplot2_2.0.0

loaded via a namespace (and not attached):
 [1] labeling_0.3     colorspace_1.2-6 scales_0.3.0     plyr_1.8.3       tools_3.2.3      gtable_0.1.2     Rcpp_0.12.3      grid_3.2.3      
 [9] digest_0.6.9     munsell_0.4.3

Can't install cowplot in RStudio R 3.1.2

install.packages("cowplot", repos="http://cran.r-project.org/")
Installing package into '/project/csbio/wwang/Rpackages'
(as 'lib' is unspecified)
Warning message:
package 'cowplot' is not available (for R version 3.1.2)

R CMD check with dev ggplot2

I see:

checking examples ... ERROR
Running examples in ‘cowplot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_sub
> ### Title: Add annotation underneath a plot
> ### Aliases: add_sub
> 
> ### ** Examples
> 
> p1 <- ggplot(mtcars, aes(mpg, disp)) + geom_line(colour = "blue") + background_grid(minor='none')
> ggdraw(add_sub(p1, "This is an annotation.\nAnnotations can span multiple lines."))
Warning: `axis.ticks.margin` is deprecated. Please set `margin` property  of `axis.text` instead
Error in FUN(X[[i]], ...) : 
  Theme element 'text' has NULL property: margin, debug
Calls: ggdraw ... element_render -> calc_element -> lapply -> FUN -> lapply -> FUN
Execution halted

Can you please look into ASAP? I'm submitting to CRAN on Friday

Potential feature request: dual axes

There has been some discussion of creating plots with dual axes to highlight the equivalance between scales. For example, a plot of temperature vs. time with a left axis in Celcius and the right in Fahrenheit. There have been some ok solutions like the one here and others from the SO discussion here.

Given the way the backend is set up in cowplot, would there be a good way of implementing this as a feature? If so, I'd be happy to try and help out by submitting a PR if you have a suggestion of how to implement it within the existing code.

useDingbats=FALSE causes problems on OSX/X11

Nice package! Looks to be very useful. However, the cowplot implementation of ggsave seems to cause two problems with my OSX system.

• In order to get plots to be sized correctly, I need to use ggsave(.., type="cairo"). Since the cowplot ggsave doesn't allow extra parameters to be passed through, I can't do this.
• I wrote save_plot2 to pass extra arguments through to ggsave, but I still get an error message about useDingbats:

Error in check.options(new, name.opt = ".X11.Options", envir = .X11env) : c("invalid argument name ‘useDingbats’ in 'grDevices::png(..., width = width, height = height, res = dpi, '", "invalid argument name ‘useDingbats’ in ' units = \"in\")'")

I think the problem is that only the .pdf device recognizes useDingbats in X11, attempting to use save_plot to create a png, for instance, fails.

I'd be happy to rewrite around this issue; have put in a pull request.

I'm using ggplot2 1.0.0, R 3.0.3