Error when running vignette MetENP_vignette.rmd

[biodavidjm]

I get the following error when running the last chunk of the vignette:

Plot pathway network

The pathway network is such that it shows metabolites that are connected to different pathways and same metabolite in different pathway. Color of nodes of metabolites are according to the fold change of metabolites (low expression in green and high in red) and size of pathway nodes (square nodes) are according to the number of branches (meaning no of metabolites). All metabolite are written in blue

plot_pathway_networks(met_path,kegg_es, TRUE)

Error:

Error in `geom_edge_diagonal()` at MetENP/R/plot_pathway_networks.R:67:2:
! Problem while converting geom to grob.
ℹ Error occurred in the 1st layer.
Caused by error:
! Unknown colour name: Arachidonic acid metabolism
Backtrace:
  1. base (local) `<fn>`(x)
  2. ggplot2:::print.ggplot(x)
  4. ggplot2:::ggplot_gtable.ggplot_built(data)
  5. ggplot2:::by_layer(...)
 12. ggplot2 (local) f(l = layers[[i]], d = data[[i]])
     ...
 20. self$draw_panel(...)
 21. ggraph (local) draw_panel(..., self = self)
 25. scales::alpha(data$edge_colour, data$edge_alpha)
 26. farver::decode_colour(colour, alpha = TRUE)
 27. farver:::decode_c(...)

Error in geom_edge_diagonal(aes_(colour = ~category), alpha = 0.8, show.legend = FALSE) : 
  
ℹ Error occurred in the 1st layer.
Caused by error:
! Unknown colour name: Arachidonic acid metabolism

[mano-at-sdsc]

I have fixed the issue in Jupyter notebooks by updating the source file plot_pathway_networks.R; will check if it is fixed in rmd as well.

[mano-at-sdsc]

The rmd file has been updated.