Help with 3d scatter plot
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Zhiyuan Tian
Sep 22, 2016, 8:07:44 PM9/22/16
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Hello, I got a code online to make a 3D plot like this
library(plotly)
plot_ly(data = iris, x = Sepal.Length, y = Sepal.Width, z = Petal.Width, color = Species, type = "scatter3d", mode = "markers")
However, I met a problem when I run it
Error in as.character(tools:::httpdPort) :
cannot coerce type 'closure' to vector of type 'character'
Does anyone know how to deal with this?
Thanks ahead!!! 
Brandon Hurr
Sep 22, 2016, 9:23:22 PM9/22/16
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Zhiyuan,
Firstly, this stuff is under very active development so stuff is changing more rapidly than most can keep up with (except the developers). I say this mainly because the way you reference variables appears to be as expressions.
In ?plot_ly, it shows this in the examples.
plot_ly(z = ~volcano, type = "surface")
So, I rewrote your statement with that in mind and I got a plot.
plot_ly(data = iris, x = ~Sepal.Length, y = ~Sepal.Width, z = ~Petal.Width, color = ~Species, type = "scatter3d", mode = "markers")
It would very much help if we knew what version of the various packages you are using if this does not solve your problem.
B
devtools::session_info()
Session info -----------------------------------------------------------------------------------
setting value
version R version 3.3.1 Patched (2016-06-22 r70818)
system x86_64, darwin13.4.0
ui AQUA
language (EN)
collate en_US.UTF-8
tz America/Los_Angeles
date 2016-09-22
Packages ---------------------------------------------------------------------------------------
package * version date source
assertthat 0.1 2013-12-06 CRAN (R 3.3.0)
base64enc 0.1-3 2015-07-28 CRAN (R 3.3.0)
colorspace 1.2-6 2015-03-11 CRAN (R 3.3.0)
curl 2.0 2016-09-17 cran (@2.0)
DBI 0.5-1 2016-09-10 cran (@0.5-1)
devtools 1.11.1.9000 2016-06-23 Github (hadley/devtools@d247c17)
digest 0.6.10 2016-08-02 cran (@0.6.10)
dplyr * 0.5.0.9000 2016-09-23 Github (hadley/dplyr@6153e13)
ggplot2 * 2.1.0.9000 2016-09-23 Github (hadley/ggplot2@70ae16c)
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)
htmlwidgets 0.7 2016-08-02 cran (@0.7)
httr 1.2.1 2016-07-03 cran (@1.2.1)
jsonlite 1.1 2016-09-14 cran (@1.1)
knitr 1.13 2016-05-09 CRAN (R 3.3.0)
lazyeval 0.2.0.9000 2016-09-23 Github (hadley/lazyeval@c155c3d)
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)
plotly * 4.5.0 2016-09-23 Github (ropensci/plotly@66039c8)
plyr 1.8.4 2016-06-08 CRAN (R 3.3.0)
purrr 0.2.2.9000 2016-09-23 Github (hadley/purrr@8c72c35)
R6 2.1.3 2016-08-19 cran (@2.1.3)
RColorBrewer 1.1-2 2014-12-07 CRAN (R 3.3.0)
Rcpp 0.12.7 2016-09-05 cran (@0.12.7)
scales 0.4.0 2016-02-26 CRAN (R 3.3.0)
tibble 1.2-12 2016-09-23 Github (hadley/tibble@6d2bb08)
tidyr 0.6.0.9000 2016-09-23 Github (hadley/tidyr@3c9335b)
viridisLite 0.1.3 2016-03-12 cran (@0.1.3)
withr 1.0.2 2016-06-20 CRAN (R 3.3.0)
yaml 2.1.13 2014-06-12 CRAN (R 3.3.0)
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Zhiyuan Tian
Sep 23, 2016, 7:37:02 PM9/23/16
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Hi Brandon,
Thanks for you help! I run the rewrite code and get another error like this:
Error in unique.default(cols) : unique() applies only to vectors
The version of package you mean R version? When I using ??plot_ly, it shows example like this:
data(economics, package = "ggplot2")
p <- plot_ly(economics, x = date, y = uempmed, type = "scatter",
showlegend = FALSE)
So maybe we are in the different version of R?
Thanks again for helping,
Tina
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Michael Hannon
Sep 24, 2016, 12:44:17 AM9/24/16
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I think that Brandon is asking for you to show us the output of the function "session_info()" as run on your computer. Here's an example from my computer:
> library(plotly)
Loading required package: ggplot2
Attaching package: ‘plotly’
The following object is masked from ‘package:ggplot2’:
last_plot
The following object is masked from ‘package:graphics’:
layout
> library(devtools)
>
> session_info()
Session info -----------------------------------------------------------------------------------
setting value
version R version 3.3.1 (2016-06-21)
system x86_64, linux-gnu
ui X11
language en_US
collate en_US.UTF-8
tz <NA>
date 2016-09-23
Packages ---------------------------------------------------------------------------------------
package * version date source
assertthat 0.1 2013-12-06 CRAN (R 3.2.1)
base64enc 0.1-3 2015-07-28 CRAN (R 3.2.2)
colorspace 1.2-6 2015-03-11 CRAN (R 3.2.0)
devtools * 1.12.0 2016-06-24 CRAN (R 3.3.1)
digest 0.6.10 2016-08-02 CRAN (R 3.3.1)
ggplot2 * 2.1.0 2016-03-01 CRAN (R 3.2.4)
gridExtra 2.2.1 2016-02-29 CRAN (R 3.2.3)
gtable 0.2.0 2016-02-26 CRAN (R 3.2.3)
htmltools 0.3.5 2016-03-21 CRAN (R 3.2.4)
htmlwidgets 0.7 2016-08-02 CRAN (R 3.3.1)
httr 1.2.1 2016-07-03 CRAN (R 3.3.1)
jsonlite 1.0 2016-07-01 CRAN (R 3.3.1)
magrittr 1.5 2014-11-22 CRAN (R 3.2.0)
memoise 1.0.0 2016-01-29 CRAN (R 3.2.3)
munsell 0.4.3 2016-02-13 CRAN (R 3.2.3)
plotly * 3.6.0 2016-05-18 CRAN (R 3.3.1)
plyr 1.8.4 2016-06-08 CRAN (R 3.3.0)
R6 2.1.3 2016-08-19 CRAN (R 3.3.1)
Rcpp 0.12.7 2016-09-05 CRAN (R 3.3.1)
scales 0.4.0 2016-02-26 CRAN (R 3.2.3)
tibble 1.2 2016-08-26 CRAN (R 3.3.1)
tidyr 0.6.0 2016-08-12 CRAN (R 3.3.1)
viridis 0.3.4 2016-03-12 CRAN (R 3.2.4)
withr 1.0.2 2016-06-20 CRAN (R 3.3.1)
>
Zhiyuan Tian
Sep 24, 2016, 7:29:50 PM9/24/16
to davi...@googlegroups.com
Thanks for explanation! Here is my output for running the package "plotly"
> library(plotly)
Loading required package: ggplot2
Attaching package: ‘plotly’
The following object is masked from ‘package:ggplot2’:
last_plot
The following object is masked from ‘package:graphics’:
layout
Warning messages:
1: package ‘plotly’ was built under R version 3.2.5
2: package ‘ggplot2’ was built under R version 3.2.5
I still got the error like this:
> plot_ly(data = iris, x = Sepal.Length, y = Sepal.Width, z = Petal.Width, color = Species, type = "scatter3d", mode = "markers")
Error in as.character(tools:::httpdPort) :
cannot coerce type 'closure' to vector of type 'character'
Some guess for why this happened?
Tina
Brandon Hurr
Sep 24, 2016, 8:16:43 PM9/24/16
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Your R is out of date by about 4 months so there could be something there.
Could you run the following in an empty R session and paste the output into your reply:
library(plotly)
sessionInfo()
I suspect you just have some out of date code. My first step would be updating R by downloading the latest (3.3.1).
After install you'll need to reinstall your packages (I think).
A suggestion:
install.packages("tidyverse")
install.packages("plotly")
This should get you mostly back to where you want to be (assuming you like the tidyverse) for this question.
Then try your code again and if you still have issues email back with the sessionInfo() requested above.
B
Zhiyuan Tian
Sep 24, 2016, 9:36:28 PM9/24/16
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I update the R to 3.3.1, and the plot is showing! Thank you so much :-P
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