Convert module to microtable object (trans_comm)

[anabelvonjackowski]

Dear microeco team,

What an incredible package you have built!

I am trying to construct a network with the end goal of running the plot_spe_func_perc. section Explainable-class of the tutorial (v1.4.0)

My code is as follows:

micro <- phyloseq2meco(all_data) otu_table_16S <- micro$otu_table taxonomy_table_16S <- micro$tax_table taxonomy_table_16S_tidy <- taxonomy_table_16S %>% tidy_taxonomy sample_info_16S <- micro$sample_table[,c(1:11)] env_data_16S <-micro$sample_table[,-c(1:11)]

dataset <- microtable$new(sample_table = sample_info_16S, otu_table = otu_table_16S, tax_table = taxonomy_table_16S) dataset$filter_pollution(taxa = c("mitochondria", "chloroplast"))

use tidy_dataset() to make OTUs and samples information consistent across files dataset$tidy_dataset()

create trans_network object t1 <- trans_network$new(dataset = dataset, cal_cor = "base", taxa_level = "OTU", filter_thres = 0.000001, cor_method = "spearman")

create correlation network t1$cal_network(p_thres = 0.01, COR_cut = 0.7) t1$res_network

add modules t1$cal_module() t1$res_network convert module info to microtable object meco_module <- t1$trans_comm(use_col = "module")

running the trans_comm, I get the following error "Run get_node_table function to get the node property table ... Error in get(as.character(FUN), mode = "function", envir = envir) : object 'FUN' of mode 'function' was not found"

but when I run get_node_table(node_roles = TRUE) I receive the same error: Error in get(as.character(FUN), mode = "function", envir = envir) : object 'FUN' of mode 'function' was not found

I have been searching through trans_network.R for the longest time and cant figure out what my mistake is. Would you happen to know?

Thanks and best regards, Anabel

[ChiLiubio]

Hi. Could you please attach your t1 so that I can reproduce your issue? To save it, please follow the steps in the tutorial (https://chiliubio.github.io/microeco_tutorial/notes.html#save-function) and attach the compressed object.

Best, Chi

[anabelvonjackowski]

Dear Chi, The t1 is attached- Thanks for your help :-) vonjackowski_t1_test.RData.zip

[ChiLiubio]

Hi. I run those steps and find it is ok. Could you please recreate an R project and try to run these steps again?

library(microeco)
load("vonjackowski_t1_test.RData")
t1$cal_module()
t1$get_node_table()
meco_module <- t1$trans_comm(use_col = "module")

[anabelvonjackowski]

Hi Chi,

I did. After the trans_comm(use_col = "module") function I get the following error: "No sample_table provided, automatically use colnames in otu_table to create one ...", which is weird cause I do have t1$sample_table, right?

vonjackowski_t1_test_v2.zip

[ChiLiubio]

Hi. This is a message, not an error. The message is inside the microtable class and invoked when no sample_table is provided. The sample_table in t1 is for samples, but the sample names in created microtable is each module name, not the sample names. So the following analysis will do not need metadata.

[ChiLiubio]

So you can view the automatically created sample_table in the result, i.e. View(meco_module$sample_table).