Errors in visualization step

[Suhail221107]

Dear contributors,
I was testing the steps in advance usage section of the package using the given example data. I could easily generate the heatmap and bubble plots. However, I encounter the errors during below steps:

Save the heatmap

p=HeatmapRBP(res=res,rbp_lfc=rbp_lfc)
n=length(p$tree_row$order)
pdf(location,length(names(res)))
p
dev.off()
Error in p$tree_row : $ operator not defined for this S4 class

Draw network of the RBP that are most changing or choose specific RBPs

Draw_network_by_group(regulators=rbp_lfc,res=res,Targets=Targets,gene_groups=gene_groups,n=5,forwarded = F)
Error in ggnet2(new_adj, size = sizes, color = node_color, label = c(RBP_kept, :
could not coerce net to a network object

I would higjhly appreciate if you could please suggest for possible reason or solution of above two errors.

Best regards,
Suhail

[baptiste-ker]

Dear Suhail,

Thank you for pointing out the error.
About the heatmap saving step. We corrected on the readme the line
n=length(p$tree_row$order)
and replaced with
n=length(p@ht_list$RBP direction@matrix)

About the network, we acknowledge the error you encounter. In the installation phase of CLIPreg, it is important to note that the "network" package must be of version 1.16.1 as written in the readme
devtools::install_version("network", version = "1.16.1", repos = "http://cran.us.r-project.org")

Unfortunately, this package has been updated while CLIPreg was developed and does not work with the most recent updates of the package "network".

We hope that helps you.

Best,
Baptiste