Volcano plot pathway names

[ChristinaSchmidt1]

In the Volcano plot function we have specific pathway names within the plot. We need to change this, so the users pathway names are automatically used.

[dprymidis]

Done.

I added the safe_colorblind_palette which we use for the Alluvial plot adn added some adittional colors to be safe that they are more than the pathways. We have the parameter Input data which has the data and Input_Pathways which must have a column Metabolite and Pathway. It can be the same input as the Input_data is we added Input in the DMA function, or it can be a separate dataframe If we want to check another pathway list. It takes and assignes a color to each metabolite based on the pathway it falls into from the pathways in the Input_Pathway dataframe.

[ChristinaSchmidt1]

Thanks, this looks nice! Lets add to "Check input files" a warning/stop that more pathways than colours are present and recommend to summarise sub-pathways together where possible. (Sorry if this is somewhere in the code and I missed it; I just searched for warnings and stops).

[dprymidis]

I added this: (lines 795-797 in Visualization) if (length(unique(Input_pathways$Pathway)) > length(safe_colorblind_palette)){ stop(" The maximum number of pathways in the Input_pathways must be less than ",length(safe_colorblind_palette),". Please summarize sub-pathways together where possible and repeat.") }

the safe_colorblind_palette is the colors we use.

[ChristinaSchmidt1]

Thank you!