Error : object 'Coryz' not found

[MingyuYang-Yale]

Hi,

I am encountering an issue:

Initially, when I ran the following code:

engep_predict <- engep_predict(osmfish,ref_list,pre_genes)

I got error message:

I modified the code as follows (per you suggested)

engep_predict <- engep_predict(osmfish,ref_list,pre_genes,parallel=T,get_baes=T,get_weight=T,
                              simi_list = c("pearson", "spearman", "cosine", "jaccard", "weighted_rank",
                                            "manhattan", "canberra", "euclidean"))

This solve the initial issue, However, when I ran the following code:

gene_expressions = as.data.frame(engep_predict)

I encountered another error:

This is my installation code:

conda create -y -n ENGEP r-base r-essentials r-devtools
conda activate ENGEP
devtools::install_github("tpq/propr")
devtools::install_github("Zhangxf-ccnu/ENGEP")

Could you please provide guidance on how to resolve this issue?

Thank you!

[Japrin]

The same problem with you @MingyuYang-Yale

Try this: gene_expressions = as.data.frame(engep_predict$ensemble$exp)

[MingyuYang-Yale]

The same problem with you @MingyuYang-Yale

Try this: gene_expressions = as.data.frame(engep_predict$ensemble$exp)

Thank you so much! Your previous solution worked perfectly.

However, I've encountered another issue: the error message saying, "could not find function plot_exp_pattern."

Do you know how I can resolve this?

Thank you in advance for your help!

[st-yang97]

Thank you for reaching out and bringing this issue to our attention.

For the first error (gene_expressions = as.data.frame(engep_predict)), we have updated the examples in our GitHub repository.

For the second question, we have not integrated the functions used in downstream experiments into the R package. However, you can find these functions in this directory. You can call the functions by sourcing the function files or by directly running the function code before calling the functions.

source('.../code/plotting.R')

I hope this helps you. Please feel free to reach out if you have any further questions or concerns.