I am trying to create a 3-D graph (using scatter3d) and save the graph to a file
so I can insert the graph into a manuscript. I am able to create the graph. When
I run the code below an RGL window opens that has the graph. The file is saved
to disk after dev.odd() runs. Unfortunately, when I open the saved file, all I
see is a white window. Can someone tell me how to have the file so I can
subsequently read and place the file in a paper? The problem occurs regardless
of the format in which I try to save the file, e.g. png, tiff.
x <- 1:10
y <- 2:11
z <- y+rnorm(10)
ForGraph<-data.frame(x=x,y=y,z=z)
ForGraph
gpathj <- file.path("C:","LAL","test.jpeg")
gpathj
jpeg(file = gpathj)
par(mai = c(0.5, 0.5, 0.5, 0.5))
scatter3d(z=ForGraph$x,
y=ForGraph$y,
x=ForGraph$z,
surface=FALSE,grid=TRUE,sphere.size=4
,xlab="Categories",ylab="ScoreRange",
zlab="VTE Rate (%)",axis.ticks=TRUE)
dev.off()
Thank you,
John
[[alternative HTML version deleted]]
The simple solution for Windows is to use (windows icon) + shift + s. You then
select a portion of your screen and it gets copied to your clipboard. You can
then paste that into your document. Of course this will not work if it is
important that the reader is able to rotate the graphic.
Tim
-----Original Message-----
From: R-help <r-help-bounces at r-project.org> On Behalf Of Sorkin, John
Sent: Wednesday, January 5, 2022 2:46 PM
To: r-help at r-project.org (r-help at r-project.org) <r-help at
r-project.org>
Subject: [R] Save a graph file use jpeg(file=file)
[External Email]
I am trying to create a 3-D graph (using scatter3d) and save the graph to a file
so I can insert the graph into a manuscript. I am able to create the graph. When
I run the code below an RGL window opens that has the graph. The file is saved
to disk after dev.odd() runs. Unfortunately, when I open the saved file, all I
see is a white window. Can someone tell me how to have the file so I can
subsequently read and place the file in a paper? The problem occurs regardless
of the format in which I try to save the file, e.g. png, tiff.
x <- 1:10
y <- 2:11
z <- y+rnorm(10)
ForGraph<-data.frame(x=x,y=y,z=z)
ForGraph
gpathj <- file.path("C:","LAL","test.jpeg")
gpathj jpeg(file = gpathj) par(mai = c(0.5, 0.5, 0.5, 0.5))
scatter3d(z=ForGraph$x,
y=ForGraph$y,
x=ForGraph$z,
surface=FALSE,grid=TRUE,sphere.size=4
,xlab="Categories",ylab="ScoreRange",
zlab="VTE Rate (%)",axis.ticks=TRUE)
dev.off()
Thank you,
John
[[alternative HTML version deleted]]
______________________________________________
R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dhelp&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=9PEhQh2kVeAsRzsn7AkP-g&m=9AMmnr8IGTA1cG1beZmaYb3IDwiObdbc6OI3PkjbwbniR_W4i9hcMzYbyzYTE-gS&s=2IkUWGiufhME4qqOuIRPGShSOMTsStDDwSkLoTt4zdM&ePLEASE
do read the posting guide
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.R-2Dproject.org_posting-2Dguide.html&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=9PEhQh2kVeAsRzsn7AkP-g&m=9AMmnr8IGTA1cG1beZmaYb3IDwiObdbc6OI3PkjbwbniR_W4i9hcMzYbyzYTE-gS&s=NHEqSQ0hFwKq_5lC0CqVYr53rYXLTpdWVNXZMCEMLLI&eand
provide commented, minimal, self-contained, reproducible code.
On 05/01/2022 2:45 p.m., Sorkin, John wrote:> I am trying to create a 3-D graph (using scatter3d) and save the graph to a file so I can insert the graph into a manuscript. I am able to create the graph. When I run the code below an RGL window opens that has the graph. The file is saved to disk after dev.odd() runs. Unfortunately, when I open the saved file, all I see is a white window. Can someone tell me how to have the file so I can subsequently read and place the file in a paper? The problem occurs regardless of the format in which I try to save the file, e.g. png, tiff. > > > x <- 1:10 > y <- 2:11 > z <- y+rnorm(10) > ForGraph<-data.frame(x=x,y=y,z=z) > ForGraph > > gpathj <- file.path("C:","LAL","test.jpeg") > gpathj > jpeg(file = gpathj) > par(mai = c(0.5, 0.5, 0.5, 0.5)) > scatter3d(z=ForGraph$x, > y=ForGraph$y, > x=ForGraph$z, > surface=FALSE,grid=TRUE,sphere.size=4 > ,xlab="Categories",ylab="ScoreRange", > zlab="VTE Rate (%)",axis.ticks=TRUE) > dev.off() > >You didn't say what package you found scatter3d in, but you did say it opens an rgl window. rgl doesn't use R graphics devices, so jpeg() and the like don't work. To save an rgl image, you use the rgl::snapshot3d() function. It only has support for saving to PNG format. If you are writing your manuscript in R Markdown or knitr Rnw, there are ways to have the file included automatically. There have been methods to use with Sweave as well, but those aren't being maintained: people should use knitr instead. Duncan Murdoch
Tim
Thank you for your suggestion. The problem with your suggestion is that the
copied image is low resolution, 96dpi. Saved files can have higher resolution.
Thank you
John
John David Sorkin M.D., Ph.D.
Professor of Medicine
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology and Geriatric
Medicine
Baltimore VA Medical Center
10 North Greene Street<x-apple-data-detectors://12>
GRECC<x-apple-data-detectors://12> (BT/18/GR)
Baltimore, MD 21201-1524<x-apple-data-detectors://13/0>
(Phone) 410-605-711<tel:410-605-7119>9
(Fax) 410-605-7913<tel:410-605-7913> (Please call phone number above prior
to faxing)
On Jan 5, 2022, at 2:59 PM, Ebert,Timothy Aaron <tebert at ufl.edu> wrote:
?The simple solution for Windows is to use (windows icon) + shift + s. You then
select a portion of your screen and it gets copied to your clipboard. You can
then paste that into your document. Of course this will not work if it is
important that the reader is able to rotate the graphic.
Tim
-----Original Message-----
From: R-help <r-help-bounces at r-project.org> On Behalf Of Sorkin, John
Sent: Wednesday, January 5, 2022 2:46 PM
To: r-help at r-project.org (r-help at r-project.org) <r-help at
r-project.org>
Subject: [R] Save a graph file use jpeg(file=file)
[External Email]
I am trying to create a 3-D graph (using scatter3d) and save the graph to a file
so I can insert the graph into a manuscript. I am able to create the graph. When
I run the code below an RGL window opens that has the graph. The file is saved
to disk after dev.odd() runs. Unfortunately, when I open the saved file, all I
see is a white window. Can someone tell me how to have the file so I can
subsequently read and place the file in a paper? The problem occurs regardless
of the format in which I try to save the file, e.g. png, tiff.
x <- 1:10
y <- 2:11
z <- y+rnorm(10)
ForGraph<-data.frame(x=x,y=y,z=z)
ForGraph
gpathj <- file.path("C:","LAL","test.jpeg")
gpathj jpeg(file = gpathj) par(mai = c(0.5, 0.5, 0.5, 0.5))
scatter3d(z=ForGraph$x,
y=ForGraph$y,
x=ForGraph$z,
surface=FALSE,grid=TRUE,sphere.size=4
,xlab="Categories",ylab="ScoreRange",
zlab="VTE Rate (%)",axis.ticks=TRUE)
dev.off()
Thank you,
John
[[alternative HTML version deleted]]
______________________________________________
R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__stat.ethz.ch_mailman_listinfo_r-2Dhelp%26d%3DDwICAg%26c%3DsJ6xIWYx-zLMB3EPkvcnVg%26r%3D9PEhQh2kVeAsRzsn7AkP-g%26m%3D9AMmnr8IGTA1cG1beZmaYb3IDwiObdbc6OI3PkjbwbniR_W4i9hcMzYbyzYTE-gS%26s%3D2IkUWGiufhME4qqOuIRPGShSOMTsStDDwSkLoTt4zdM%26e%3D&data=04%7C01%7Cjsorkin%40som.umaryland.edu%7C9e6f54c1880f46b971f608d9d085e667%7C717009a620de461a88940312a395cac9%7C0%7C0%7C637770095783063118%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=g0489Q9jetIGpbYyjL%2FY2LTKxKud5r4EnFoDlP6uO5c%3D&reserved=0
PLEASE do read the posting guide
https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__www.R-2Dproject.org_posting-2Dguide.html%26d%3DDwICAg%26c%3DsJ6xIWYx-zLMB3EPkvcnVg%26r%3D9PEhQh2kVeAsRzsn7AkP-g%26m%3D9AMmnr8IGTA1cG1beZmaYb3IDwiObdbc6OI3PkjbwbniR_W4i9hcMzYbyzYTE-gS%26s%3DNHEqSQ0hFwKq_5lC0CqVYr53rYXLTpdWVNXZMCEMLLI%26e%3D&data=04%7C01%7Cjsorkin%40som.umaryland.edu%7C9e6f54c1880f46b971f608d9d085e667%7C717009a620de461a88940312a395cac9%7C0%7C0%7C637770095783063118%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=8vRn%2FuQJVjFydNfiXOQKIyYBDM3EXXBdBRCccHQnvWY%3D&reserved=0
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]