chiliubio / microeco_tutorial

Documentation for microeco package

microeco_tutorial

This book gives comprehensive tutorials of the microeco package. The tutorial is available at https://chiliubio.github.io/microeco_tutorial/.

Citation

Chi Liu, Yaoming Cui, Xiangzhen Li, Minjie Yao, microeco: an R package for data mining in microbial community ecology, FEMS Microbiology Ecology, Volume 97, Issue 2, February 2021, fiaa255, https://doi.org/10.1093/femsec/fiaa255

Contributing

We welcome any contribution on the package development and tutorial documentation ! Any idea/suggestion will be considered. By participating in this project you agree to abide by the terms outlined in the Contributor Code of Conduct.

microeco_tutorial's Issues

error in code

Dear Chi
Hope you are fine and doing good
I am trying to load a file and it is giving an error
otu_table <- read.csv("C:/Users/muneerm/Desktop/Correlation/otu_table.csv", row.names = "X")
Error in data[[rowvar]] : attempt to select less than one element in get1index--
Although this is an irrelevant error on part of this tutorial, but I hope you can help me to get out of iit
thanks and regards

error in analysis

Dear Sir
I trust you are fine and keeping good.
Thank you so much for your help time and again.
I am now trying to analyze a new dataset, once I uploaded the same and started the analysis and ran the code.
dataset$ tidy_dataset()
No same sample name found between rownames of sample table and colnames of otu table.
then when I checked the otu table and sample table found this difference.
However, when checking in the .csv files the x is not there Infront of the sample names.
I think the issue may be because of this we have different names.
How to manage this
Kindly please suggest
thanks and regards.
otu_table.csv
sample_info.csv

Couldn't find the function:phyloseq2meco()

Dear Chi

Thank you for developing this great package.

But I didn't manage to convert my phyloseq object to microeco object because I didn't find the phyloseq2meco() function in the package (I read it from the tutorial:https://chiliubio.github.io/microeco_tutorial/file2meco-package.html#phyloseq).

Could you please tell me is the function still there or how should I convert it manually if I have to ?

Thank you and best regards,
Jay

Post-hoc test with ANOVA

Thank you for making this excellent package.

Based on the source code, Dunn's test seems to be the post hoc test method after ANOVA for trans_alpha and trans_diff. I just wanted to make sure this is correct. Additionally, is it possible to use Tukey's or other tests?

Xiaoping

Error in dataset$tidy_dataset()

Hi Dear Sir
Trust you are well
First I want to know any of the paper where I can found hiw to cute different packages used in microeco package for publications.
I mean how to cite for diversity, relative abundance etc.
Second I was trying to analyze another dataset, and I got an error in running the code
dataset$tidy_dataset()
Error: No same feature names found between rownames of otu_table and rownames of taxa_table!
Please check rownames of these tables!
Kindly suggest

cal_tax4fun() showing error

Hello,

I was trying to get microorganisms' functions of the three treatments that I was interested in; the R code was able to run and showed the results with biological functions for each replicate using the following script:
t2 = trans_func$new(paolo)
t2$cal_spe_func()
t2$cal_spe_func_perc(abundance_weighted = F)
t2$plot_spe_func_perc(use_group_list = T)
Even though I got the functions within each replicate, this was not my expectations; I was expecting to get these functions within modules generated from the co-occurrence analysis using the following code

Network analysis

# Correlation based on spearman

t1 = trans_network$new(dataset = paolo, cor_method = "spearman", filter_thres = 0.0001,
taxa_level = "OTU",cal_cor = "WGCNA")

use arbitrary coefficient threshold to construct network

t1$cal_network(COR_p_thres = 0.001, COR_cut = 0.7)

# Calling unidirected network

t1$cal_module(method = "cluster_fast_greedy", module_name_prefix = "M")

Save network

t1$cal_network_attr()

After all, I was expecting a clear repartition of functions within treatments but I couldn't load the reference folder SILVA123 (unzipped) which was saved on my local drive. By running the following script
t3 = trans_func$new(dataset = paolo)
t3$cal_tax4fun(folderReferenceData = "C:/Users/ngeme/Documents/SILVA123")
the script run into the following error:
Error in dimnames(x) <- dn :
length of 'dimnames' [1] not equal to array extent
Could you please help me out.
Thank you. Find the attached dataset I was using
paolo.zip

Tax4Fun2 Error

I get the following error message with Tax4Fun2:
"Error in t1$cal_tax4fun2(blast_tool_path = "ncbi-blast-2.5.0+/bin", path_to_reference_data = "Tax4Fun2_ReferenceData_v2", :
Tax4Fun2 ReferenceData folder--test_prediction is not existed!"

Initially I had this error on my own data so I attempted to run the microeco-tutorial.Rmd and got the same error.

Error in creating a trans_abund object

Hi @ChiLiubio
Hope you are doing good
I am following the tutorial and getting through the codes and overcoming the errors.
Now While trying to plot a relative abundance, I am getting an error
I ran the code
abundance<- trans_abund$new(dataset = dataset, taxrank = "Phylum", ntaxa = 10)
It gave an error object "trans_abund" not found.
However, I have calculated the abundance using dataset$cal_abund()