I have created a complex SVG file with scientific data: https://svgshare.com/s/TcX . The individual plots were generated as PDFs by the original data analysis software (FlowJo), I imported them separately and made some minor modifications (resizing, adjusting alignment etc.).
When I export the figure from Inkscape as a PDF, the small dots are lost and some plots get an unwanted black background: https://pdfhost.io/v/HAndEZSsd_nucleigatingpdf.pdf
Is there a way to export the figure without it getting changed, or can I modify some objects so that they are not problematic to export? I would ideally like to export the figure as PDF, as I want to import it into a Latex document, but other vector formats might also be ok.
If I export als PNG the figure comes out correctly (but I need a vector format).
Update: If I ungroup all the objects and export as PDF, the dots appear but are blurred: https://pdfhost.io/v/gIOby7gcM_nucleigatingtestpdf.pdf
Solution: I solved the problem by going to the original file exported from FlowJo, removing all groups and masks, and copying the embedded raster images into my layout. Then the PDF export worked correctly.