It seems the plotting tools only support output to file. In a markdown context the user is thus forced to use markdown syntax:
to import the graphics into a markdown report. This image import tag lacks control over image size and I find KEGG graphs import in postage stamp size. Sending output directly to the console would allow utilization of chunk options to control the output and resolution when including graphics in markdown reports.
Along the same lines, wherever ggplot is used for the graphics, returning the ggplot object would be most convenient. This would give the user the opportunity to further customize/annotate these plots before printing/saving and would allow the use of the ggsave function to provide finer control over size, dpi and file format.
Many of the dotplots would be improved by utilization of transparency to better interpret regions where many pathway points overlap.
Lastly, for interactive plots, showing the pathway name in a mouseover would be highly desirable.
It seems the plotting tools only support output to file. In a markdown context the user is thus forced to use markdown syntax:
to import the graphics into a markdown report. This image import tag lacks control over image size and I find KEGG graphs import in postage stamp size. Sending output directly to the console would allow utilization of chunk options to control the output and resolution when including graphics in markdown reports.
Along the same lines, wherever ggplot is used for the graphics, returning the ggplot object would be most convenient. This would give the user the opportunity to further customize/annotate these plots before printing/saving and would allow the use of the ggsave function to provide finer control over size, dpi and file format.
Many of the dotplots would be improved by utilization of transparency to better interpret regions where many pathway points overlap.
Lastly, for interactive plots, showing the pathway name in a mouseover would be highly desirable.
Best, John Thompson (BMS)