Getting error when running "plot_connections" function

[chao lu]

Hi！I am trying to run Cicero on some single cell ATACseq data from Gossypium hirsutum (using this pipline:https://cole-trapnell-lab.github.io/cicero-release/docs_m3/) and am having some trouble with adapting it for the Gossypium hirsutum genome and annotations. Briefly, the problem is related to "plot_connections" function in the R package. While I ran the function in my R console, there was always a warning saying "error: gene_model is not a data frame". To troubleshoot and debug the problem, I used print fucntion in R and the results showed that gene_model was indeed a data frame with 843673 rows and 15 columns, which was contradictory to the warning. Does any one had this issue before. Any help would be much appreciated.

                                                                                                                                                                                                                                                                    Thank you,

                                                                                                                                                                                                                                                                      Best Regards,

                                                                                                                                                                                                                                                                      Emory Lucas

[Hannah Pliner]

Hi,

DataFrame and data.frame are actually different classes (confusingly). You should be able to convert to a data frame using as.data.frame!

Best,

Hannah