After exporting an image as .pdf the following error message is shown when opening the file in Adobe Acrobat.
After closing the message, the pdf works like normal. However, this is not optimal if these files should be included as supplementary files for a publication.
There’s an exception and that is when exporting a PCoA figure. The figure is not shown at all in the .pdf file, even after closing the error message.
I will look into this. Can you give me more info about the OS that you are running this on? I have tried to recreate the problem under MacOS and under Windows 10, but failed to trigger the problem.
An alternative way to generate a PDF is to print to a PDF file, if you OS supports that.
Windows 10 and Adobe Acrobat Pro
It worked when I used print-> Adobe PDF
When I used print -> Microsoft Print to PDF the quality of the pdf file was very low.
I want to ask another question here, in the KEGG pathway map I guess each box shows the number of reads per sample, but how can I know the maximum number on the y-axis for each box? Is this number the same for all boxes?
All boxes in the same pathway are on the same scale.
The scaling is such that the largest value is scaled to fill the height of a box and all other values are scaled accordingly.
Be aware that there are three different settings for the scale, which
you can set in the middle of the tool bar, using the buttons that show a linear plot, sqrt plot and log plot. These control whether the bars are on a linear, sqrt or log scale (sqrt=square root is the default).
In this example, the box numbered 22.214.171.124 has the largest number and all counts are shown on a linear scale:
Thanks for the reply and clarification. Is it possible to get the y-axis scale with printed labels? I wish to include that in my figure for each pathway I decide to analyze. I can easily add such a scale in the legend or ontop of the figure using Adobe Illustrator, however currently I don’t know the scale labels. Where e.g. is 1000 reads, 10 000 reads, or 100 000 reads on the y-axis? Or is it possible to show this somehow in %? Then the maximum on the y-axis for each box would be 100%. I would only need this scale once on one of the boxes or below the figure, as I understood each box have the same y-axis for each KEGG pathway map.
I am not sure if this kind of figure could be accepted by a reviewer without indicating the labels on the y-axis, and make it clear what the y-axis shows.
Would this suit your purposes? I print the type of scaling (Lin., Sqrt or Log), draw a box
and show the value associated with the box height. This is the max value seen anywhere on the pathway. See the red circle in this figure:
If this suits your needs, then I will build a new release with this added to the visualization of KEGG pathways.
Thanks for the update, this is definitely an improvement and would be very useful when using the Linear scaling. However, for the other scaling methods (sqrt and log) which I found to be very useful when visualizing the data there would need to be indications on the y-axis on the box in the new top left legend (e.g. a tick mark line at 5, 50, 500 reads count etc). Another option I can think of, that might be easier to implement, is by adding more of these boxes with the representative read value to the top left legend that you made. Each box could be filled according to the y-axis scale of the scaling method. One box would e.g. be filled by 5 reads, the other one 50 reads, 500 reads, and so on. Or simply four boxes with 25%, 50%, 75%,100% filled based on the maximum value. And then the read value right next to each box. This would help a reader to approximate how many reads each sample represents even on a sqrt or log scale. What do you think, would it work?
I did look into the second idea, but it was quite clunky… but I will give it another go
thanks for looking into this. If it’s not possible to add this to the image, it would be great if this information (y-axis labels) was available for the user. Because I could also add it to the figure caption describing how many reads the y-axis shows at e.g. the top, mid, and bottom, maybe even also the 25% and 75% mark, a bit clunky but it could do. I could also add such a scale in Illustrator or some other software if I knew the labels on the y-axis for each pathway.
How about this: I think it works:
Yes this works! Thanks for adding this information to the kegg pathway maps. Will this be included in the next update?
I will build a new release tomorrow or Monday at the latest