dplyr masks GGally and breaks ggparcoord
Given a fresh session, executing a small ggparcoord(.) example provided in the documentation of the function
library(GGally)
data(diamonds, package="ggplot2")
diamonds.samp <- diamonds[sample(1:dim(diamonds)[1], 100), ]
ggparcoord(data = diamonds.samp, columns = c(1, 5:10))
results into the following plot:
Again, starting in a fresh session and executing the same script with the loaded dplyr
library(GGally)
library(dplyr)
data(diamonds, package="ggplot2")
diamonds.samp <- diamonds[sample(1:dim(diamonds)[1], 100), ]
ggparcoord(data = diamonds.samp, columns = c(1, 5:10))
results in:
Error: (list) object cannot be coerced to type 'double'
Note that the order of the library(.) statements does not matter.
Questions
I need both dplyr and ggparcoord(.) in a bigger analysis but this minimal example reflects the problem i am facing.
Versions
UPDATE
To wrap the excellent answer given by Joran up:
Answers
Working code sample:
library(GGally)
library(dplyr)
data(diamonds, package="ggplot2")
diamonds.samp <- diamonds[sample(1:dim(diamonds)[1], 100), ]
ggparcoord(data = as.data.frame(diamonds.samp), columns = c(1, 5:10))
Converting my comments to an answer...
The GGally package here is making the reasonable assumption that using [ on a data frame should behave the way it always does and always has. However, this all being in the Hadley-verse, the diamonds data set is a tbl_df as well as a data.frame .
When dplyr is loaded, the behavior of [ is overridden such that drop = FALSE is always the default for a tbl_df . So there's a place in GGally where data[,"cut"] is expected to return a vector, but instead it returns another data frame.
...specifically, the error is thrown in your example while attempting to execute:
data[, fact.var] <- as.numeric(data[, fact.var]).
Since data[,fact.var] remains a data frame, and hence a list, as.numeric won't work.
As for your conclusion that this isn't a bug, I'd say....maybe. Probably. At least there probably isn't anything the GGally package author ought to do to address it. You just have to be aware that using tbl_df 's with non-Hadley written packages may break things.
As you noted, removing the extra class attributes fixes the problem, as it returns R to using the normal [ method.
Workaround: coerce your data for ggparcoord to as.data.table(...) or as.data.table(... , keep.rownames=TRUE) unless you want to lose all your rownames.
Cause: as per @joran's investigating, when dplyr is loaded, tbl_df overrides [ so that drop = FALSE.
Solution: file a pull-request on GGally.
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