I am new in R and getting output(images/ interactive plots) displayed by some packages in viewer pane. I would rather like them to be displayed in the ramrkdown notebook.
Here is an example, using magick::image_read() which displays image in viewer pane and not inline:
Reference link where a knitted document has produced images within the notebook using same package as I have used: https://cran.r-project.org/web/packages/magick/vignettes/intro.html
Below are the settings I am using:
Have asked similar question on keras package earlier How to make plots appear in Rmarkdown file instead of viewer pane when working with keras in Rstudio?
This is happening with some of the packages, how do I make these images/plots appear inline ?
I am attempting to render a powerpoint presentation from rmarkdown.
I downloaded this powerpoint template and associated files from sol-eng and am able to generate the powerpoint as is.
However, if I open the template and do
view -> slide master
and adjust any of the slide master (i.e. change the background color)
close slide master -> save
I get the error "The file may be damaged or it may have been created in a pre-release version of PowerPoint." when I attempt to render the powerpoint.
I am unclear why using the template as is vs changing the background would generate an error in making the powerpoint presentation.
Any suggestions would be helpful:)
it might be that R writes binary differently than Powerpoint. Is it possible to create a ioslide or beamer slide file with the original powerpoint file instead? If you do IOSlides or beamer, the view with only need a web browser and could be a more flexible file for presentation
I used a different computer/version of powerpoint; adjusted the master slide and now it works - still unsure why I couldn't adjust with my version of powerpoint so I am guessing some versioning issue.
When I create plots within a single chunk of an R-Studio markdown file, they appear in a nice array with clickable thumbnails:
However, when I publish as an HTML file, these figures are simply displayed vertically, one after the other. Is there any way to achieve the way that it originally looks in RStudio?
Unfortunately there's no way to output what RStudio shows you, but you can do this and a lot of other HTML formatting yourself using the knitrBootstrap package.
Check out the end of this example for a clickable-thumbnail example.
I created a report that contain a Pichart, Histogram and DatePicker, I want to export this report with those components.
Any idea how to do it?
icCube has a print report, but there is nothing to export a full report to an image, it's a pdf.
You can use your browser and print to pdf as an option. You might want to play a bit with css and media to make parts of the page not visible on printing ( see ).
I have an ipython notebook with an embedded image from my local drive. I was expecting it to be embedded in the JSON along with the output of code cells, but when I distributed the notebook, the image did not appear to users. What is the recommended way (or ways) to embed an image in a Notebook, so that it doesn't disappear if users rerun code cells, clear cell output, etc.?
The notebook system caches images included with , but they last only until the python "kernel" serving the notebook is restarted. If I rename the image file on disk, I can close and reopen the notebook and it still shows the image; but it disappears when I restart the kernel.
Edit: If I generate an image as code cell output and then export the notebook to html, the image is embedded in the html as encoded data. Surely there must be a way to hook into this functionality and load the output into a markdown (or better yet "raw nbconvert") cell?
from IPython.display import Image
Image(filename='imagename.png')
will be exported (with ipython nbconvert) to html that contains the following:
<div class="output_png output_subarea output_execute_result">
<img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAnAAAAFgCAYAAAA...
</div>
However, even when I manually embedded this snippet into a markdown cell, I couldn't get the image to display. What am I doing wrong?
Update (2020)
Apparently, the problem has (finally!) been addressed in the newer notebook / Jupyter versions: as of 2018 (thanks for the link #Wayne), the html sanitizer will accept an embedded html image, as in <img src="data:image/png;base64,iV...> . Markdown image syntax also accepts images as embedded data, so there are two ways to do this. Details in these helpful answers:
markdown image syntax (answer by #id01)
html element syntax (in answer by #tel -- note that it works now!)
Are you happy to use an extra code cell to display the image? If so, use this:
from IPython.display import Image
Image(filename="example.png")
The output cell will have the raw image data embedded in the .ipynb file so you can share it and the image will be retained.
Note that the Image class also has a url keyword, but this will only link to the image unless you also specify embed=True (see the documentation for details). So it's safer to use the filename keyword unless you are referring to an image on a remote server.
I'm not sure if there is an easy solution if you require the image to be included in a Markdown cell, i.e. without a separate code cell to generate the embedded image data. You may be able to use the python markdown extension which allows dynamically displaying the contents of Python variables in markdown cells. However, the extension generates the markdown cells dynamically, so in order to retain the output when sharing the notebook you will need to run ipython nbconvert --to notebook original_notebook.ipynb --output preprocessed_notebook using the preprocessor pymdpreprocessor.py as mentioned in the section "Installation". The generated notebook then has the data embedded in the markdown cell as an HTML tag of the form <img src="data:image/png;base64,..."> so you can delete the corresponding code cell from preprocessed_notebook.ipynb. Unfortunately, when I tried this the contents of the <img> tag weren't actually displayed in the browser, so not sure if this is a viable solution. :-/
A different option would be to use the Image class in a code cell to generate the image as above, and then use nbconvert with a custom template to remove code input cells from the notebook. See this thread for details. However, this will strip all code cells from the converted notebook, so it may not be what you want.
The reason why the
<img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAnAAAAFgCAYAAAA...
tag doesn't do anything when you put it in a markdown cell is because IPython uses an HTML sanitizer (something called Google Caja) that screens out this type of tag (and many others) before it can be rendered.
The HTML sanitizer in IPython can be completely disabled by adding the following line to your custom.js file (usually located at ~/.ipython/profile_default/static/custom/custom.js):
iPython.security.sanitize_html = function (html) { return html; };
It's not a great solution though, as it does create a security risk, and it doesn't really help that much with distribution.
Postscript:
The ability to render base64 encoded strings as images != obvious security concern, so there should be a way for the Caja people to eventually allow this sort of thing through (although the related feature request ticket was first opened back in 2012, so don't hold your breath).
I figured out that replacing the image URL in the  with a base64 URL, similar to the ones found above, can embed an image in a markdown container.
Example markdown:
If using the IPython HTML() function to output raw HTML, you can embed a linked image in base64 inside an <img> tag using the following method:
import base64
import requests
from IPython.core.display import HTML
def embedded_image(url):
response = requests.get(url)
uri = ("data:" +
response.headers['Content-Type'] + ";" +
"base64," + str(base64.b64encode(response.content).decode('utf-8')))
return uri
# Here is a small example. When you export the notebook as HTML,
# the image will be embedded in the HTML file
html = f'<img src="{embedded_image("https://upload.wikimedia.org/wikipedia/commons/5/56/Kosaciec_szczecinkowaty_Iris_setosa.jpg")}" />'
HTML(html)
UPDATE: As pointed out by #alexis, this doesn't actually answer the question correctly, this will not allow users to re-run cells and have images persist (this solution only allows one to embed the images into exports).
As of Jupyter Notebook 5, you can attach image data to cells, and refer to them from the cell via attachment:<image-file-name>. See the menu Edit > Insert Image, or use drag and drop.
Unfortunately, when converting notebooks with attached (embedded) images to HTML, those images will not show up.
To get them into the HTML code, you can use (for instance) nbtoolbelt.
It will replace those attachment: references by data: with the image data embedded in the img tag.