process map output in R

[RijinM]

Hello everyone,

So I have created a process map using R for a sample dataset. I have also placed the code in the R View node. Currently, the map gets outputted locally on my computer but I would like to connect the image output directly into another KNIME node. For example, the image output widget. I am confused as to how exactly can I get the map to go into the image output of the R-View node. Since process maps are not graphs, I can’t use the plot command in R . It would be great if someone can help me out. Thanks!

[aworker]

Hi @RijinM and welcome to the KNIME community forum

Maybe this previous post by @stelfrich could shed some light on how to solve your problem:

R view (Table) image tiff or jpeg

Hi @CarolinaPR, You can use KNIME Image Processing to save images into different formats: You’ll have to convert the output image port of the R View (Table) into a column and, subsequently, convert the column to a KNIME Image Processing type before you can export to JPEG and TIFF. Here’s a workflow that demonstrates this: Best regards, Stefan

29902 – stelfrich

Hope it helps.

Best
Ael

[RijinM]

Hi,
Thank you for your help! I tried the workflow posted but is there a way of directly outputting an image rather than a plot from the R-View node. Because, the R code output that I have is a process map which is an image and does not have x,y, or title so I can’t use qplot, or plot commands in general as that give me an error in KNIME.

[mlauber71]

@RijinM maybe you could give us an example what kind of graphic is being produced. Maybe a small workflow without any secret data.

You could use the png() command from within the R node but that might als involve plotting.

library(Cairo)

# https://stackoverflow.com/questions/24999983/r-unable-to-start-device-png-capabilities-has-true-for-png
png(my_path,width=1024,height=768, bg = "transparent", type="cairo")
plot.new

# your plot here

dev.off()

examples of Venn gramms – mlauber71

You also can handle images that are on your drive if they are SVG or PNG and bring them back into KNIME and work further with them:

Image Writer Help

@badger101, @aworker this workflow would demonstrate how to list a bunch of PNG files and then give them a new name and save them to another folder. [image] You might want to download the whole workflow group. It’s from a german introduction into KNIME but I think the functions should be clear:

[RijinM]

Thank you for your help! For my workflow, I just have a csv reader → R_View → image output widget.

In terms of what kind of graphic is being produced from my R View node, an example of this can be found here:ggplot2 - Creating Process Map Diagrams using different packages in R - Stack Overflow

The issue I am facing is how can I get this graphic as an actual image output so it can be passed into the next node in KNIME. Right now, I have a render_graph command in my script which renders this graph somewhere on my computer. I can’t seem to access the location. I tried other commands in R such as export_graph but that doesn’t seem to work. If I try plotting it, I get the following error since the map is not a plot

[aworker]

Hi @RijinM

@mlauber71 provided in another post a solution for what I believe the solution you need. The R code is the following:

which you can find in the solution posted by @mlauber71 at the following link:

various methods to export data and graphics from KNIME with R – mlauber71

I tried it and the only thing i needed to change (because I’m working on Windows) is the way the folder separator is coded (from // to \). The fully run version compatible with windows is available from the following link:

k_001_r_export_data.knwf (232.0 KB)

Please have a look at the -R- code inside the -R- nodes of this workflow which I believe should solve your problem.

Hope it helps,
Ael

[RijinM]

Thank you for your help!