R help - May 2010 - geom_ribbon removes missing values

Hi everyone,

it looks like geom_ribbon removes missing values and plots a single
ribbon over the whole interval of x values. However, I'd rather want it
to act like geom_line, that is, interrupt the ribbon for the interval of
missing values and continue once there are new values. Here's an example:

library(ggplot2)
df <- data.frame(
  date = seq(from = as.Date("2010-05-15"),
             to = as.Date("2010-05-24"),
             by = "1 day"),
  low = c(4, 5, 4, 5, NA, NA, 4, 5, 4, 5),
  mid = c(8, 9, 8, 9, NA, NA, 8, 9, 8, 9),
  high = c(12, 13, 12, 13, NA, NA, 12, 13, 12, 13))
ggplot(df, aes(x = date, y = mid, ymin = low, ymax = high)) +
  geom_line() +
  geom_ribbon(fill = alpha("blue", 0.5))

When running this code, R tells me:

Warning message:
Removed 2 rows containing missing values (geom_ribbon).

When you look at the graph, you can see that the line stops at May 18
and starts again on May 21. But the ribbon reaches from May 15 to 24,
even though there are no values on May 19 and 20.

Is there an option that I could set? Or a geom/stat that I should use
instead? In my pre-ggplot2 times I used polygon(), but I figured there
must be something better in ggplot2 (as there has always been so far).

Thanks,
--Karsten

Hi Karsten,

There's no easy way to do this because behind the scenes geom_ribbon
uses grid.polygon.

Hadley

On Sun, May 30, 2010 at 7:26 AM, Karsten Loesing
<karsten.loesing at gmx.net> wrote:
> Hi everyone,
>
> it looks like geom_ribbon removes missing values and plots a single
> ribbon over the whole interval of x values. However, I'd rather want it
> to act like geom_line, that is, interrupt the ribbon for the interval of
> missing values and continue once there are new values. Here's an
example:
>
> library(ggplot2)
> df <- data.frame(
> ?date = seq(from = as.Date("2010-05-15"),
> ? ? ? ? ? ? to = as.Date("2010-05-24"),
> ? ? ? ? ? ? by = "1 day"),
> ?low = c(4, 5, 4, 5, NA, NA, 4, 5, 4, 5),
> ?mid = c(8, 9, 8, 9, NA, NA, 8, 9, 8, 9),
> ?high = c(12, 13, 12, 13, NA, NA, 12, 13, 12, 13))
> ggplot(df, aes(x = date, y = mid, ymin = low, ymax = high)) +
> ?geom_line() +
> ?geom_ribbon(fill = alpha("blue", 0.5))
>
> When running this code, R tells me:
>
> Warning message:
> Removed 2 rows containing missing values (geom_ribbon).
>
> When you look at the graph, you can see that the line stops at May 18
> and starts again on May 21. But the ribbon reaches from May 15 to 24,
> even though there are no values on May 19 and 20.
>
> Is there an option that I could set? Or a geom/stat that I should use
> instead? In my pre-ggplot2 times I used polygon(), but I figured there
> must be something better in ggplot2 (as there has always been so far).
>
> Thanks,
> --Karsten
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>


-- 
Assistant Professor / Dobelman Family Junior Chair
Department of Statistics / Rice University
http://had.co.nz/

Hi William,

On 6/10/10 2:07 AM, William Dunlap wrote:
> I'm not sure exactly what you want in poly_ids, but
> if x is a vector of numbers that might contain NA's
> and you want a vector of integers that identify each
> run of non-NA's and are NA for each then you can get
> it with
>     poly_id <- cumsum(is.na(x)) + 1 # bump count for each NA seen
>     poly_id[is.na(x)] <- NA
> E.g.,
>   > x<-c(1.5, 2.5, NA, 4.5, 5.5, 6.5, NA, 8.5, 9.5, NA, NA, 12.5)
>   > poly_ids <- cumsum(is.na(x)) + 1
>   > poly_ids[is.na(x)] <- NA
>   > rbind(x, poly_ids) # to line up input and output
>            [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11]
> [,12]
>   x         1.5  2.5   NA  4.5  5.5  6.5   NA  8.5  9.5    NA    NA
> 12.5
>   poly_ids  1.0  1.0   NA  2.0  2.0  2.0   NA  3.0  3.0    NA    NA
> 5.0

Great! That's exactly what I want in poly_ids. Thanks! Please find the
new patch below.

I also put a new branch on GitHub that is based on ggplot2 master and
that has this patch. Note that I still don't know how to run ggplot2
from sources, so you'll have to trust in my copy-and-paste fu:

  http://github.com/kloesing/ggplot2/commit/177e69ae654da074



--- ggplot2-orig	2010-06-06 14:02:25.000000000 +0200
+++ ggplot2	2010-06-10 08:31:02.000000000 +0200
@@ -5044,9 +5044,16 @@


   draw <- function(., data, scales, coordinates, na.rm = FALSE, ...) {
-    data <- remove_missing(data, na.rm,
-      c("x","ymin","ymax"), name =
"geom_ribbon")
     data <- data[order(data$group, data$x), ]
+
+  # Instead of removing NA values from the data and plotting a single
+  # polygon, we want to "stop" plotting the polygon whenever
we're missing
+  # values and "start" a new polygon as soon as we have new values. 
We do
+  # this by creating an id vector for polygonGrob that has distinct
+  # polygon numbers for sequences of non-NA values and NA for NA values in
+  # the original data.  Example: c(NA, 2, 2, 2, NA, NA, 4, 4, 4, NA)
+  poly_ids <- cumsum(is.na(data$ymin) | is.na(data$ymax)) +1
+  poly_ids[is.na(data$ymin) | is.na(data$ymax)] <- NA

     tb <- with(data,
       coordinates$munch(data.frame(x=c(x, rev(x)), y=c(ymax,
rev(ymin))), scales)
@@ -5054,12 +5061,12 @@

     with(data, ggname(.$my_name(), gTree(children=gList(
       ggname("fill", polygonGrob(
-        tb$x, tb$y,
+        tb$x, tb$y, id=c(poly_ids, rev(poly_ids)),
         default.units="native",
         gp=gpar(fill=alpha(fill, alpha), col=NA)
       )),
       ggname("outline", polygonGrob(
-        tb$x, tb$y,
+        tb$x, tb$y, id=c(poly_ids, rev(poly_ids)),
         default.units="native",
         gp=gpar(fill=NA, col=colour, lwd=size * .pt, lty=linetype)
       ))

Best,
--Karsten