The following two lines of code, taken from this script, do what I think they should; that is, use a previously generated ggplot file - gganim - create an animation in Rstudio's viewer (the first line) and save the last animation to the graphics directory on my mac (the second line). But my mac thinks this is a txt file. I've tried adding .mpeg, mp4, etc. to the file name without any success. Seems like one of this problems I'll do a Homer Simpson on after someone points out the solution.
gganimate::animate(gganim, nframes = length(yearsToDisplay), fps = 1, renderer = ffmpeg_renderer())
gganimate::anim_save("animateOutput", animation = last_animation(), path = "graphics")
After some more experimentation, I discovered that the following modifications to the two lines work; that is, I explicitly specify the file format in the ffmpeg_render function and in the anim_save file name
gganimate::animate(gganim, format = "mp4", nframes = length(yearsToDisplay), fps = 1, renderer = ffmpeg_renderer(format = "mp4"))
gganimate::anim_save("animateOutput.mp4", animation = last_animation(), path = "graphics")
Related
I've created an excel template for reporting. In the excel file, there will be some images. I'm able to insert the images by using openxlsx package.
test.fpath <-'Templates/CB.xlsx'
wb <- openxlsx::loadWorkbook(test.fpath)
insertImage(wb, sheet = 1, file = "tm_player_image.png",startRow = 8, startCol = 3, width = 1.1, height = 1.73, units = "in")
saveWorkbook(wb, file = "createWorkbookExample.xlsx", overwrite = TRUE)
openxlsx package allows you to set specific value for starting row and column. When I run the script, excel file is saved like the following image.
First position of the image
However, I don't want the image start row = 8 and col = 3. I should able to drag the image where ever I want and define top-left position values. Is there any way to achieve this?
Adjusted position of the image
I need to define position of the image like this.
Left (Sol): 13,64''
Top (Üst): 0,74''
Thanks for your help.
It is possible, but there is no function to do this and AFAIK Excel positions are always relative to the screen and OS one is using. Therefore you have to use a bit try and error to get the correct positions.
Have a look at wb$drawings[[1]][[1]]. The content is an XML string. You are looking for the xdr:from part (as seen below). You have to adjust xdr:colOff and xdr:rowOff like in the example below. I had to insert a fairly high value to see any impact.
<xdr:from xmlns:xdr="http://schemas.openxmlformats.org/drawingml/2006/spreadsheetDrawing">\n
<xdr:col xmlns:xdr="http://schemas.openxmlformats.org/drawingml/2006/spreadsheetDrawing">2</xdr:col>\n
<xdr:colOff xmlns:xdr="http://schemas.openxmlformats.org/drawingml/2006/spreadsheetDrawing">50000</xdr:colOff>\n
<xdr:row xmlns:xdr="http://schemas.openxmlformats.org/drawingml/2006/spreadsheetDrawing">4</xdr:row>\n
<xdr:rowOff xmlns:xdr="http://schemas.openxmlformats.org/drawingml/2006/spreadsheetDrawing">40000</xdr:rowOff>\n
</xdr:from>
I'm creating a script to cluster my data in a server. I need to save the text output and the images as well. The text output works just fine but when I try to use the png() + plot() + dev.off() thing to save the plots, no image is created.
[ADDED FOR CLARIFICATION]
What I need to do is to SAVE the plot (i.e. generate an image file) in running mode. If I run the code step by step, the file is created.
I already tried to change the image format to PDF and JPG using the corresponding functions but I'm still getting no images as output when running the code as script. When stepping, it works great.
Since it takes a little while for R to render the image when I'm running step by step, I tried to add Sys.sleep(2) in between commands (code below) but nothing changed.
I think the problem might be related to the package that I'm using and the type of object it generates (library(NMF)). I looked at the documentation to see if there was something about the way the plot() function works with the type of object that the clustering algorithm generates but the text is vague:
"The result (of estim.r <- nmf(esGolub, 2:6, nrun=10, seed=123456) for example) is a S3 object of class NMF.rank, that contains a data.frame with the quality measures in column, and the values of r in row. It also contains a list of the consensus matrix for
each value of r".
"All the measures can be plotted at once with the method plot (Figure 1), and the function consensusmap generates heatmaps of the consensus matrix for each value of the rank".
There is another type of image that can be generated after the clustering runs: the consensusmap. This one works on both cases (stepping and running).
The script is pretty short. Here it is:
library(NMF)
data = read.csv('R.csv', header=TRUE, sep=";")
res1 <- nmf(data, rank=2:5, nrun=1, "brunet", "random")
# this always works
capture.output(summary(res1) ,file = "summary.txt", append = TRUE)
# this always works too
png(filename = 'consensus.png', width = 1366, height = 768, units = 'px')
consensusmap(res1)
dev.off()
# this does not work on 'running mode', only 'stepping mode'
png(filename = 'metrics.png', width = 1366, height = 768, units = 'px')
# added hoping it would fix the issue. It didn't
Sys.sleep(2)
plot(res1)
# added hoping it would fix the issue. It didn't
Sys.sleep(2)
dev.off()
The summary.txt file is generated, the consensus.png too. The metrics.png is not. What's going on here??
I have made a beautiful plot in R to be used in a scientific journal. According to the journal's specifications, I need an eps file format with embedded fonts. Since R does not export eps files with embedded fonts, I am using the base graphics call embedFonts() to convert it. However, this call is changing the bounding box of my figure. In this simple example below, the white space is cropped. In my OCD-adjusted publication-quality plot, white space is added because I've already adjusted it perfectly to the edges.
I want the fonts to be embedded, but everything else to stay the same!
Here is an example:
setEPS()
postscript(file = "~/Desktop/test.eps", family = "Helvetica", colormodel = "srgb", width = 5, height = 3)
plot(x = 1:10, y = 1:10, col = "red", main = "Keep everything the same but embed my fonts!")
dev.off()
embedFonts(file = "/Users/athena/Desktop/test.eps", format = "eps2write", outfile = "/Users/athena/Desktop/stupid.eps")
So far I have:
- installed ghostscript using homebrew: $ brew install ghostscript
- learned that embedFonts needs FULL paths, no tilda's allowed
- specified the format as "eps2write" because the default "ps2write" changes it to a postscript
I spent so much effort on "reproducible research" with open data, open code, open journal, bla bla bla... I really don't want to have to make my final figures using illustrator conversion or something :(
The reason this happens is because embedFonts internally calls Ghostscript which in turn tries to act smart by fitting an "optimal" bounding box by trimming out some of the surrounding white space.
We can prevent that by drawing an invisible box around the perimeter of our 5inx3in drawing area in R. Just add one more line to your code snippet:
setEPS()
postscript(file = "~/Desktop/test.eps", family = "Helvetica", colormodel = "srgb", width = 5, height = 3)
plot(x = 1:10, y = 1:10, col = "red", main = "Keep everything the same but embed my fonts!")
box(which="outer", col="white")
dev.off()
embedFonts(file = "/Users/athena/Desktop/test.eps", format = "eps2write", outfile = "/Users/athena/Desktop/stupid.eps")
Another way to go about this is Jonathan's answer here which basically uses sed to read in Bounding Box info from the input file and writes it to the output file: http://r.789695.n4.nabble.com/eps-file-with-embedded-font-td903387.html as pointed out by #neilfws in a comment above.
I have been following a basic manual of Maxima, I need to solve a differencial ecuation system.
First of all, I loaded both of the packets, load(dynamics); and load(draw);
In order to obtain the points I have:
solutionsPoints: rk([4-x^2-4*y^2,y^2-x^2+1],[x,y],[-1.25,0.75],[t,0,4,0.02]);
I got all the points needed, now to represent this,
draw3d(points_joined = true, point_type = dot, points(solutionsPoints), terminal = eps);
Maxima in this case returns:
[gr3d(points)]
What should I do to have this representation?
Thanks
I see that you have terminal = eps, therefore draw3d will create a .eps file and it won't display the image. I tried draw3d as you showed it, and it created maxima_out.eps in the current directory, and I can use a viewer (I used evince) to look at it, and it seems OK.
If you cut out the terminal = eps part, it will display the curve immediately, without creating an output file.
I would like to print multiple graphs in one pdf file. I know there has been a lot on this, but I would like to print different window/graph sizes for each page, i.e. first page a 8.5x11, second page 11x8.5 and so on. I tried this:
pdf(file="Combined_Graphs.pdf",onefile=TRUE,bg="white",width=8.5,height=11)
hist(rnorm(100))
pdf(file="Combined_Graphs.pdf",onefile=TRUE,width=11, height=8.5, bg="white")
hist(rnorm(100,10,2),col="blue")
dev.off()
I must be using onefile=TRUE wrong as it only generates the last graphic before closing. Is there a better way to size the graphic device without having to call the pdf function twice?
What I would do is produce seperate PDF's and them combine them later. I use the PDF toolkit for this. Wrapping this in an R function using a system call through system even makes it scriptable from R. The call to pdftk will look something like:
pdftk *pdf cat output combined.pdf
or in R:
system("pdftk *pdf cat output combined.pdf")
combine_pdfs = function(path, output_pdf) {
system(sprintf("pdftk %s/*pdf cat output %s"), path, output_pdf)
}
I think what you are trying to do cannot be done in R, i.e., you need to use external tools such as the PDF toolkit as suggested by Paul Hiemstra to combine separate PDF files with varying page dimensions (an alternative tool is PDFjam).
If you set onefile = TRUE in your call to pdf(), each plot that is written to that PDF device will be printed on a separate page, yet with the same page dimensions. In your example, you open a first PDF device, write one plot to it, then you open a second PDF device, write a different plot to it, and then close the second PDF device but leave the first PDF device open. Since you use the same file argument for both pdf() calls, you might not notice that the first PDF device is still open. If you closed it, only the first plot would end up in "Combined_Graphs.pdf".
Here is a modified version of your example that illustrates how PDF devices are opened, filled with content, and closed:
pdf(file = "foo.pdf", onefile = TRUE, width = 8.5, height = 11)
hist(rnorm(100))
hist(rnorm(100, 10, 2), col = "red")
pdf(file = "bar.pdf", width =11, height = 8.5)
hist(rnorm(100, 10, 2), col = "blue")
dev.off()
dev.off()