Error in dataset$tidy_dataset()

[Muneer111]

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

[ChiLiubio]

Hi. For the measures of alpha and beta diversity, please use command like citation("vegan"). There is no need for the relative abundance. I also got your point about the citation of other method or part. I will take some time to collect such citations and descriptions in the tutorial soon after. Thanks! Please check whether your feature names are different between your otu_table and tax_table.

Chi

[Muneer111]

Dear Sir i trust you are doing good I have an error in a code I tried to run t1$cal_autocor()
plot: [1,2] [==>--------------------------------------------------] 6% est: 2s Error in cor.test.default(x, y, method = method, use = use) : not enough finite observations Please suggest or any alternative to calculate correlation thanks and regards

[ChiLiubio]

Hi, It seems like the effective samples are not enough. How about sending your data to me to have a try?

Best, Chi

[Muneer111]

Dear Professor I hope you are doing well I have a shotgun metagenome dataset analyzed by SqueezeMeta, and I have analyzed the taxonomic part using microecopackage. I need to know how to use this package for functional parts such as PFAM, COG, and KEGG. Second, I have RNA datasets; can I use this package to analyze the same? Again, I have to plot ARGs and VFs also how to plot that any package or online software for that and Finally, in this project I have sampled from different countries, I want to plot some networking, I tried but i am not getting the proper one, please guide me in this, I want the one that is mentioned in this tutorial Kindly pease help me here and guide for these queries Thanking in advance Regards

On Tue, 10 Oct 2023 at 06:53, Chi Liu @.***> wrote:

Hi, It seems like the effective samples are not enough. How about sending your data to me to have a try?

Best, Chi

— Reply to this email directly, view it on GitHub https://github.com/ChiLiubio/microeco_tutorial/issues/13#issuecomment-1754161507, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASJLNJOYI7IH5DJAKLLPO3LX6SPQRAVCNFSM6AAAAAA4DO47CWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONJUGE3DCNJQG4 . You are receiving this because you authored the thread.Message ID: @.***>

-- Your's Sincerely Dr. Muneer Ahmad Ph.D. Research Scholar Dr. H S G Central University, Sagar (470003) M.P

[ChiLiubio]

Hi. As there are no specific method or design for the metagenomic or RNA data, you should select and use the current methods in the functions to perform the analysis you need. To read those data, please operate the gene abundance files just like the amplicon data.

[Muneer111]

Dear Professor Thank you So much for your prompt response Will do as advised by you. I also have some more queries Currently I am analysis a datasets with two type of samples surface water and microplastic each collected from 4 different sites and across two different seasons. So, I want to know first to analysis site wise in microplastic and surface water and then between seasons. And as requested, I need guidance in network analysis. Thanks and Regards

On Sat, 9 Dec, 2023, 10:39 am Chi Liu, @.***> wrote:

Hi. As there are no specific method or design for the metagenomic or RNA data, you should select and use the current methods in the functions to perform the analysis you need. To read those data, please operate the gene abundance files just like the amplicon data.

— Reply to this email directly, view it on GitHub https://github.com/ChiLiubio/microeco_tutorial/issues/13#issuecomment-1848327954, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASJLNJJG35U4RMHGMOZUQDLYIQPS3AVCNFSM6AAAAAA4DO47CWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNBYGMZDOOJVGQ . You are receiving this because you authored the thread.Message ID: @.***>

[Muneer111]

Dear Professor Hope you are doing well Besides the above queries, I was running a code and I got this error

t1$plot_bar(others_color = "grey70", facet = "Group", xtext_keep = FALSE, legend_text_italic = FALSE)

Input colors are not enough to use. Add more colors automatically via color interpolation ...

Kindly please guide me how to add more colors

Regards and Thanks

On Sat, 9 Dec 2023 at 14:41, Muneer Malla @.***> wrote:

Dear Professor Thank you So much for your prompt response Will do as advised by you. I also have some more queries Currently I am analysis a datasets with two type of samples surface water and microplastic each collected from 4 different sites and across two different seasons. So, I want to know first to analysis site wise in microplastic and surface water and then between seasons. And as requested, I need guidance in network analysis. Thanks and Regards

On Sat, 9 Dec, 2023, 10:39 am Chi Liu, @.***> wrote:

Hi. As there are no specific method or design for the metagenomic or RNA data, you should select and use the current methods in the functions to perform the analysis you need. To read those data, please operate the gene abundance files just like the amplicon data.

— Reply to this email directly, view it on GitHub https://github.com/ChiLiubio/microeco_tutorial/issues/13#issuecomment-1848327954, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASJLNJJG35U4RMHGMOZUQDLYIQPS3AVCNFSM6AAAAAA4DO47CWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNBYGMZDOOJVGQ . You are receiving this because you authored the thread.Message ID: @.***>

-- Your's Sincerely Dr. Muneer Ahmad Ph.D. Research Scholar Dr. H S G Central University, Sagar (470003) M.P

[Muneer111]

Dear Professor

This error also popped up

Kindly help with these issues

Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : namespace ‘rlang’ 1.1.0 is already loaded, but >= 1.1.1 is required

On Sun, 10 Dec 2023 at 04:51, Muneer Malla @.***> wrote:

Dear Professor Hope you are doing well Besides the above queries, I was running a code and I got this error

t1$plot_bar(others_color = "grey70", facet = "Group", xtext_keep = FALSE, legend_text_italic = FALSE)

Input colors are not enough to use. Add more colors automatically via color interpolation ...

Kindly please guide me how to add more colors

Regards and Thanks

On Sat, 9 Dec 2023 at 14:41, Muneer Malla @.***> wrote:

Dear Professor Thank you So much for your prompt response Will do as advised by you. I also have some more queries Currently I am analysis a datasets with two type of samples surface water and microplastic each collected from 4 different sites and across two different seasons. So, I want to know first to analysis site wise in microplastic and surface water and then between seasons. And as requested, I need guidance in network analysis. Thanks and Regards

On Sat, 9 Dec, 2023, 10:39 am Chi Liu, @.***> wrote:

Hi. As there are no specific method or design for the metagenomic or RNA data, you should select and use the current methods in the functions to perform the analysis you need. To read those data, please operate the gene abundance files just like the amplicon data.

— Reply to this email directly, view it on GitHub https://github.com/ChiLiubio/microeco_tutorial/issues/13#issuecomment-1848327954, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASJLNJJG35U4RMHGMOZUQDLYIQPS3AVCNFSM6AAAAAA4DO47CWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNBYGMZDOOJVGQ . You are receiving this because you authored the thread.Message ID: @.***>

-- Your's Sincerely Dr. Muneer Ahmad Ph.D. Research Scholar Dr. H S G Central University, Sagar (470003) M.P

-- Your's Sincerely Dr. Muneer Ahmad Ph.D. Research Scholar Dr. H S G Central University, Sagar (470003) M.P

[ChiLiubio]

Please close the R, reopen it and reinstall rlang package.

[Muneer111]

Thank you professor Sorry to disturb again What about this error Kindly please guide Thanks and Regards

On Sun, 10 Dec, 2023, 1:21 am Muneer Malla, @.***> wrote:

Dear Professor Hope you are doing well Besides the above queries, I was running a code and I got this error

t1$plot_bar(others_color = "grey70", facet = "Group", xtext_keep = FALSE, legend_text_italic = FALSE)

Input colors are not enough to use. Add more colors automatically via color interpolation ...

Kindly please guide me how to add more colors

Regards and Thanks

On Sat, 9 Dec 2023 at 14:41, Muneer Malla @.***> wrote:

Dear Professor Thank you So much for your prompt response Will do as advised by you. I also have some more queries Currently I am analysis a datasets with two type of samples surface water and microplastic each collected from 4 different sites and across two different seasons. So, I want to know first to analysis site wise in microplastic and surface water and then between seasons. And as requested, I need guidance in network analysis. Thanks and Regards

On Sat, 9 Dec, 2023, 10:39 am Chi Liu, @.***> wrote:

Hi. As there are no specific method or design for the metagenomic or RNA data, you should select and use the current methods in the functions to perform the analysis you need. To read those data, please operate the gene abundance files just like the amplicon data.

— Reply to this email directly, view it on GitHub https://github.com/ChiLiubio/microeco_tutorial/issues/13#issuecomment-1848327954, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASJLNJJG35U4RMHGMOZUQDLYIQPS3AVCNFSM6AAAAAA4DO47CWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNBYGMZDOOJVGQ . You are receiving this because you authored the thread.Message ID: @.***>

-- Your's Sincerely Dr. Muneer Ahmad Ph.D. Research Scholar Dr. H S G Central University, Sagar (470003) M.P

[ChiLiubio]

Please open the help document and see the first parameter of the function for the color values input.

[Muneer111]

Dear Professor I trust you are keeping well Happy New Year I am writting to please provide an idea how to create a network for separate samples and habitat type. I created a network using the microeco tutorial but it includes all the samples. Secondly in the Mantels analysis I was willing to analyse the changes with respect to habitats like surface water and plastisphere not between the bacterial taxa Is there anyway to modify the dataset to perform this analysis. Kindly help Thanks and regards

On Mon, 11 Dec, 2023, 11:37 am Chi Liu, @.***> wrote:

Please open the help document and see the first parameter of the function for the color values input.

— Reply to this email directly, view it on GitHub https://github.com/ChiLiubio/microeco_tutorial/issues/13#issuecomment-1849657750, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASJLNJIFXPCAVA3FLNHJPETYI3H3ZAVCNFSM6AAAAAA4DO47CWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNBZGY2TONZVGA . You are receiving this because you authored the thread.Message ID: @.***>

[ChiLiubio]

Hi. Thanks. Please follow this part of the tutorial (https://chiliubio.github.io/microeco_tutorial/meconetcomp-package.html). It is very easy to extract samples by manipulating the sample_table as it shows.

[Muneer111]

Hi again Thank You so much, I think it requires phylogenetic tree as well

Secondly in the Mantels analysis I was willing to analyse the changes with respect to habitats like surface water and plastisphere not between the bacterial taxa Is there anyway to modify the dataset to perform this analysis. Regards

On Thu, 18 Jan 2024 at 07:43, Chi Liu @.***> wrote:

Hi. Thanks. Please follow this part of the tutorial ( https://chiliubio.github.io/microeco_tutorial/meconetcomp-package.html). It is very easy to extract samples by manipulating the sample_table as it shows. default.png (view on web) https://github.com/ChiLiubio/microeco_tutorial/assets/20815519/650b8d73-f507-4464-8077-ad94dc3799a9

— Reply to this email directly, view it on GitHub https://github.com/ChiLiubio/microeco_tutorial/issues/13#issuecomment-1897655394, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASJLNJPYHD3U3CH22S5JESTYPCAMXAVCNFSM6AAAAAA4DO47CWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOJXGY2TKMZZGQ . You are receiving this because you authored the thread.Message ID: @.***>

-- With Kind Regards Dr. Muneer Ahmad Malla Postdoctoral Researcher Institute for Water and Wastewater Technology, Durban University of Technology, Durban, (4001) S.A E.mail: @.> @. @.** Phone:+91-9622790800 Scopus Id: 57202376797 Orcid account: https://orcid.org/0000-0001-7878-6240 Google Scholar Account:* https://scholar.google.com/citations?user=hKIujOEAAAAJ&hl=en

[Muneer111]

Dear Sir Hope you are doing well Kindly please advise as mentioned in previous mail related to mantel analysis instead of microbial phyla I want to use sample groups like plastic and water. Second please guide how to develop separate networks for different sites. I tried one and it is as a whole but want it separately. Thanks and Regards

On Thu, 18 Jan, 2024, 11:51 am Muneer Malla, @.***> wrote:

Hi again Thank You so much, I think it requires phylogenetic tree as well

Secondly in the Mantels analysis I was willing to analyse the changes with respect to habitats like surface water and plastisphere not between the bacterial taxa Is there anyway to modify the dataset to perform this analysis. Regards

On Thu, 18 Jan 2024 at 07:43, Chi Liu @.***> wrote:

Hi. Thanks. Please follow this part of the tutorial ( https://chiliubio.github.io/microeco_tutorial/meconetcomp-package.html). It is very easy to extract samples by manipulating the sample_table as it shows. default.png (view on web) https://github.com/ChiLiubio/microeco_tutorial/assets/20815519/650b8d73-f507-4464-8077-ad94dc3799a9

— Reply to this email directly, view it on GitHub https://github.com/ChiLiubio/microeco_tutorial/issues/13#issuecomment-1897655394, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASJLNJPYHD3U3CH22S5JESTYPCAMXAVCNFSM6AAAAAA4DO47CWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOJXGY2TKMZZGQ . You are receiving this because you authored the thread.Message ID: @.***>

-- With Kind Regards Dr. Muneer Ahmad Malla Postdoctoral Researcher Institute for Water and Wastewater Technology, Durban University of Technology, Durban, (4001) S.A E.mail: @.> @. @.** Phone:+91-9622790800 Scopus Id: 57202376797 Orcid account: https://orcid.org/0000-0001-7878-6240 Google Scholar Account:* https://scholar.google.com/citations?user=hKIujOEAAAAJ&hl=en

[ChiLiubio]

Hi. Please use by_group parameter in the cal_mantel function for analysis of different groups. For the network for different sites. Please see the last reply. I have take an example.

[Muneer111]

Dear Sir https://github.com/ChiLiubio/microeco_tutorial/assets/20815519/8467b579-8955-45ad-a7c6-822ab398af59 I did the network, as mentioned by you, but how to plot it separately now. thanks and Regards

On Sat, 3 Feb 2024 at 07:53, Chi Liu @.***> wrote:

Hi. Please use by_group parameter in the cal_mantel function for analysis of different groups. For the network for different sites. Please see the last reply. I have take an example. 297577342-650b8d73-f507-4464-8077-ad94dc3799a9.png (view on web) https://github.com/ChiLiubio/microeco_tutorial/assets/20815519/8467b579-8955-45ad-a7c6-822ab398af59

— Reply to this email directly, view it on GitHub https://github.com/ChiLiubio/microeco_tutorial/issues/13#issuecomment-1925024865, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASJLNJKNT26ESKBVPXMFIGTYRWNTZAVCNFSM6AAAAAA4DO47CWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMRVGAZDIOBWGU . You are receiving this because you authored the thread.Message ID: @.***>

-- With Kind Regards Dr. Muneer Ahmad Malla Postdoctoral Researcher Institute for Water and Wastewater Technology, Durban University of Technology, Durban, (4001) S.A E.mail: @.> @. @.** Phone:+91-9622790800 Scopus Id: 57202376797 Orcid account: https://orcid.org/0000-0001-7878-6240 Google Scholar Account:* https://scholar.google.com/citations?user=hKIujOEAAAAJ&hl=en

[Muneer111]

Dear Sir As per your suggestions, I used by_group, please find below I tried three ways by using "Group, and also by_group, and group" t1$cal_mantel(use_measure = "Group", partial_mantel = TRUE) t2$cal_mantel(use_measure = "by_group", partial_mantel = TRUE) But got error

Error in array(x, c(length(x), 1L), if (!is.null(names(x))) list(names(x), : 'data' must be of a vector type, was 'NULL'

Please suggest

thanks

On Sat, 3 Feb 2024 at 20:14, Muneer Malla @.***> wrote:

Dear Sir

https://github.com/ChiLiubio/microeco_tutorial/assets/20815519/8467b579-8955-45ad-a7c6-822ab398af59 I did the network, as mentioned by you, but how to plot it separately now. thanks and Regards

On Sat, 3 Feb 2024 at 07:53, Chi Liu @.***> wrote:

Hi. Please use by_group parameter in the cal_mantel function for analysis of different groups. For the network for different sites. Please see the last reply. I have take an example. 297577342-650b8d73-f507-4464-8077-ad94dc3799a9.png (view on web) https://github.com/ChiLiubio/microeco_tutorial/assets/20815519/8467b579-8955-45ad-a7c6-822ab398af59

— Reply to this email directly, view it on GitHub https://github.com/ChiLiubio/microeco_tutorial/issues/13#issuecomment-1925024865, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASJLNJKNT26ESKBVPXMFIGTYRWNTZAVCNFSM6AAAAAA4DO47CWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMRVGAZDIOBWGU . You are receiving this because you authored the thread.Message ID: @.***>

-- With Kind Regards Dr. Muneer Ahmad Malla Postdoctoral Researcher Institute for Water and Wastewater Technology, Durban University of Technology, Durban, (4001) S.A E.mail: @.> @. @.** Phone:+91-9622790800 Scopus Id: 57202376797 Orcid account: https://orcid.org/0000-0001-7878-6240 Google Scholar Account:* https://scholar.google.com/citations?user=hKIujOEAAAAJ&hl=en

-- With Kind Regards Dr. Muneer Ahmad Malla Postdoctoral Researcher Institute for Water and Wastewater Technology, Durban University of Technology, Durban, (4001) S.A E.mail: @.> @. @.** Phone:+91-9622790800 Scopus Id: 57202376797 Orcid account: https://orcid.org/0000-0001-7878-6240 Google Scholar Account:* https://scholar.google.com/citations?user=hKIujOEAAAAJ&hl=en

[Muneer111]

Hi again Please ignore the last error message I tried these codes t1 <- trans_env$new(dataset = d1, env_cols = 5:10) t1$cal_mantel(use_measure = "bray", partial_mantel = TRUE, by_group = FALSE) t2 <- trans_env$new(dataset = d2, env_cols = 5:10) t2$cal_mantel(use_measure = "bray", partial_mantel = TRUE, by_group = FALSE) x1 <- data.frame(spec = "Proteobacteria", t1$res_mantel) %>% .[, c(1, 3, 6, 8)] x2 <- data.frame(spec = "Bacteroidetes", t2$res_mantel) %>% .[, c(1, 3, 6, 8)]

Error in data.frame(spec = "Bacteroidetes", t2$res_mantel) : arguments imply differing number of rows: 1, 0

How can fix this issue,

particularly how to fix [, c(1, 3, 6, 8)] values

Thanks and Regards

On Sat, 3 Feb 2024 at 20:33, Muneer Malla @.***> wrote:

Dear Sir As per your suggestions, I used by_group, please find below I tried three ways by using "Group, and also by_group, and group" t1$cal_mantel(use_measure = "Group", partial_mantel = TRUE) t2$cal_mantel(use_measure = "by_group", partial_mantel = TRUE) But got error

Error in array(x, c(length(x), 1L), if (!is.null(names(x))) list(names(x), : 'data' must be of a vector type, was 'NULL'

Please suggest

thanks

On Sat, 3 Feb 2024 at 20:14, Muneer Malla @.***> wrote:

Dear Sir

https://github.com/ChiLiubio/microeco_tutorial/assets/20815519/8467b579-8955-45ad-a7c6-822ab398af59 I did the network, as mentioned by you, but how to plot it separately now. thanks and Regards

On Sat, 3 Feb 2024 at 07:53, Chi Liu @.***> wrote:

Hi. Please use by_group parameter in the cal_mantel function for analysis of different groups. For the network for different sites. Please see the last reply. I have take an example. 297577342-650b8d73-f507-4464-8077-ad94dc3799a9.png (view on web) https://github.com/ChiLiubio/microeco_tutorial/assets/20815519/8467b579-8955-45ad-a7c6-822ab398af59

— Reply to this email directly, view it on GitHub https://github.com/ChiLiubio/microeco_tutorial/issues/13#issuecomment-1925024865, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASJLNJKNT26ESKBVPXMFIGTYRWNTZAVCNFSM6AAAAAA4DO47CWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMRVGAZDIOBWGU . You are receiving this because you authored the thread.Message ID: @.***>

-- With Kind Regards Dr. Muneer Ahmad Malla Postdoctoral Researcher Institute for Water and Wastewater Technology, Durban University of Technology, Durban, (4001) S.A E.mail: @.> @. @.** Phone:+91-9622790800 Scopus Id: 57202376797 Orcid account: https://orcid.org/0000-0001-7878-6240 Google Scholar Account:* https://scholar.google.com/citations?user=hKIujOEAAAAJ&hl=en

-- With Kind Regards Dr. Muneer Ahmad Malla Postdoctoral Researcher Institute for Water and Wastewater Technology, Durban University of Technology, Durban, (4001) S.A E.mail: @.> @. @.** Phone:+91-9622790800 Scopus Id: 57202376797 Orcid account: https://orcid.org/0000-0001-7878-6240 Google Scholar Account:* https://scholar.google.com/citations?user=hKIujOEAAAAJ&hl=en

-- With Kind Regards Dr. Muneer Ahmad Malla Postdoctoral Researcher Institute for Water and Wastewater Technology, Durban University of Technology, Durban, (4001) S.A E.mail: @.> @. @.** Phone:+91-9622790800 Scopus Id: 57202376797 Orcid account: https://orcid.org/0000-0001-7878-6240 Google Scholar Account:* https://scholar.google.com/citations?user=hKIujOEAAAAJ&hl=en

[ChiLiubio]

Please provide the data d1 and d2 (https://chiliubio.github.io/microeco_tutorial/notes.html#save-function). I will have a try.

[Muneer111]

Hi Sir Please find, and once done, Please mention the steps that are needed for future reference Kindly also suggest how to plot individual networks, I compared the networks, but now, How to plot them Thanks and Regards

On Sun, 4 Feb 2024 at 08:09, Chi Liu @.***> wrote:

Please provide the data d1 and d2 ( https://chiliubio.github.io/microeco_tutorial/notes.html#save-function). I will have a try.

— Reply to this email directly, view it on GitHub https://github.com/ChiLiubio/microeco_tutorial/issues/13#issuecomment-1925557609, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASJLNJIJLVVWST6HM6C7KGLYR3YHXAVCNFSM6AAAAAA4DO47CWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMRVGU2TONRQHE . You are receiving this because you authored the thread.Message ID: @.***>

-- With Kind Regards Dr. Muneer Ahmad Malla Postdoctoral Researcher Institute for Water and Wastewater Technology, Durban University of Technology, Durban, (4001) S.A E.mail: @.> @. @.** Phone:+91-9622790800 Scopus Id: 57202376797 Orcid account: https://orcid.org/0000-0001-7878-6240 Google Scholar Account:* https://scholar.google.com/citations?user=hKIujOEAAAAJ&hl=en

[Muneer111]

Dear Sir Hope you are fine and doing good Any updates with the datasets Thanks and Regards

On Sun, 4 Feb 2024 at 09:02, Muneer Malla @.***> wrote:

Hi Sir Please find, and once done, Please mention the steps that are needed for future reference Kindly also suggest how to plot individual networks, I compared the networks, but now, How to plot them Thanks and Regards

On Sun, 4 Feb 2024 at 08:09, Chi Liu @.***> wrote:

Please provide the data d1 and d2 ( https://chiliubio.github.io/microeco_tutorial/notes.html#save-function). I will have a try.

— Reply to this email directly, view it on GitHub https://github.com/ChiLiubio/microeco_tutorial/issues/13#issuecomment-1925557609, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASJLNJIJLVVWST6HM6C7KGLYR3YHXAVCNFSM6AAAAAA4DO47CWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMRVGU2TONRQHE . You are receiving this because you authored the thread.Message ID: @.***>

-- With Kind Regards Dr. Muneer Ahmad Malla Postdoctoral Researcher Institute for Water and Wastewater Technology, Durban University of Technology, Durban, (4001) S.A E.mail: @.> @. @.** Phone:+91-9622790800 Scopus Id: 57202376797 Orcid account: https://orcid.org/0000-0001-7878-6240 Google Scholar Account:* https://scholar.google.com/citations?user=hKIujOEAAAAJ&hl=en

-- With Kind Regards Dr. Muneer Ahmad Malla E.mail: @.> @. Phone:+91-9622790800 Scopus Id: 57202376797 Orcid account: https://orcid.org/0000-0001-7878-6240 Google Scholar Account: https://scholar.google.com/citations?user=hKIujOEAAAAJ&hl=en

[Muneer111]

Good day Dear Sir I hope you are doing well Any update related to Mantel analysis and network. Thanks and regards

On Mon, 5 Feb, 2024, 2:34 pm Muneer Malla, @.***> wrote:

Dear Sir Hope you are fine and doing good Any updates with the datasets Thanks and Regards

On Sun, 4 Feb 2024 at 09:02, Muneer Malla @.***> wrote:

Hi Sir Please find, and once done, Please mention the steps that are needed for future reference Kindly also suggest how to plot individual networks, I compared the networks, but now, How to plot them Thanks and Regards

On Sun, 4 Feb 2024 at 08:09, Chi Liu @.***> wrote:

Please provide the data d1 and d2 ( https://chiliubio.github.io/microeco_tutorial/notes.html#save-function). I will have a try.

— Reply to this email directly, view it on GitHub https://github.com/ChiLiubio/microeco_tutorial/issues/13#issuecomment-1925557609, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASJLNJIJLVVWST6HM6C7KGLYR3YHXAVCNFSM6AAAAAA4DO47CWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMRVGU2TONRQHE . You are receiving this because you authored the thread.Message ID: @.***>

-- With Kind Regards Dr. Muneer Ahmad Malla Postdoctoral Researcher Institute for Water and Wastewater Technology, Durban University of Technology, Durban, (4001) S.A E.mail: @.> @. @.** Phone:+91-9622790800 Scopus Id: 57202376797 Orcid account: https://orcid.org/0000-0001-7878-6240 Google Scholar Account:* https://scholar.google.com/citations?user=hKIujOEAAAAJ&hl=en

-- With Kind Regards Dr. Muneer Ahmad Malla E.mail: @.> @. Phone:+91-9622790800 Scopus Id: 57202376797 Orcid account: https://orcid.org/0000-0001-7878-6240 Google Scholar Account: https://scholar.google.com/citations?user=hKIujOEAAAAJ&hl=en

[Muneer111]

Dear Sir Hope you are fine and doing well Kindly please update me about the error. As I am waiting for the same Thanks and regards

On Tue, 6 Feb, 2024, 8:00 am Muneer Malla, @.***> wrote:

Good day Dear Sir I hope you are doing well Any update related to Mantel analysis and network. Thanks and regards

On Mon, 5 Feb, 2024, 2:34 pm Muneer Malla, @.***> wrote:

Dear Sir Hope you are fine and doing good Any updates with the datasets Thanks and Regards

On Sun, 4 Feb 2024 at 09:02, Muneer Malla @.***> wrote:

Hi Sir Please find, and once done, Please mention the steps that are needed for future reference Kindly also suggest how to plot individual networks, I compared the networks, but now, How to plot them Thanks and Regards

On Sun, 4 Feb 2024 at 08:09, Chi Liu @.***> wrote:

Please provide the data d1 and d2 ( https://chiliubio.github.io/microeco_tutorial/notes.html#save-function). I will have a try.

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-- With Kind Regards Dr. Muneer Ahmad Malla Postdoctoral Researcher Institute for Water and Wastewater Technology, Durban University of Technology, Durban, (4001) S.A E.mail: @.> @. @.** Phone:+91-9622790800 Scopus Id: 57202376797 Orcid account: https://orcid.org/0000-0001-7878-6240 Google Scholar Account:* https://scholar.google.com/citations?user=hKIujOEAAAAJ&hl=en

-- With Kind Regards Dr. Muneer Ahmad Malla E.mail: @.> @. Phone:+91-9622790800 Scopus Id: 57202376797 Orcid account: https://orcid.org/0000-0001-7878-6240 Google Scholar Account: https://scholar.google.com/citations?user=hKIujOEAAAAJ&hl=en

[Muneer111]

Dear Professor Trust you are doing well Any updates with Mantel Analysis. This is a bit urgent Thanks & Regards

On Tue, 6 Feb, 2024, 10:58 pm Muneer Malla, @.***> wrote:

Dear Sir Hope you are fine and doing well Kindly please update me about the error. As I am waiting for the same Thanks and regards

On Tue, 6 Feb, 2024, 8:00 am Muneer Malla, @.***> wrote:

Good day Dear Sir I hope you are doing well Any update related to Mantel analysis and network. Thanks and regards

On Mon, 5 Feb, 2024, 2:34 pm Muneer Malla, @.***> wrote:

Dear Sir Hope you are fine and doing good Any updates with the datasets Thanks and Regards

On Sun, 4 Feb 2024 at 09:02, Muneer Malla @.***> wrote:

Hi Sir Please find, and once done, Please mention the steps that are needed for future reference Kindly also suggest how to plot individual networks, I compared the networks, but now, How to plot them Thanks and Regards

On Sun, 4 Feb 2024 at 08:09, Chi Liu @.***> wrote:

Please provide the data d1 and d2 ( https://chiliubio.github.io/microeco_tutorial/notes.html#save-function). I will have a try.

— Reply to this email directly, view it on GitHub https://github.com/ChiLiubio/microeco_tutorial/issues/13#issuecomment-1925557609, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASJLNJIJLVVWST6HM6C7KGLYR3YHXAVCNFSM6AAAAAA4DO47CWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMRVGU2TONRQHE . You are receiving this because you authored the thread.Message ID: @.***>

-- With Kind Regards Dr. Muneer Ahmad Malla Postdoctoral Researcher Institute for Water and Wastewater Technology, Durban University of Technology, Durban, (4001) S.A E.mail: @.> @. @.** Phone:+91-9622790800 Scopus Id: 57202376797 Orcid account: https://orcid.org/0000-0001-7878-6240 Google Scholar Account:* https://scholar.google.com/citations?user=hKIujOEAAAAJ&hl=en

-- With Kind Regards Dr. Muneer Ahmad Malla E.mail: @.> @. Phone:+91-9622790800 Scopus Id: 57202376797 Orcid account: https://orcid.org/0000-0001-7878-6240 Google Scholar Account: https://scholar.google.com/citations?user=hKIujOEAAAAJ&hl=en

[Muneer111]

Dear Sir Kindly please update about Mantel analysis. Since I am waiting from many days. Thanks in advance Regards

On Wed, 7 Feb, 2024, 5:50 am Muneer Malla, @.***> wrote:

Dear Professor Trust you are doing well Any updates with Mantel Analysis. This is a bit urgent Thanks & Regards

On Tue, 6 Feb, 2024, 10:58 pm Muneer Malla, @.***> wrote:

Dear Sir Hope you are fine and doing well Kindly please update me about the error. As I am waiting for the same Thanks and regards

On Tue, 6 Feb, 2024, 8:00 am Muneer Malla, @.***> wrote:

Good day Dear Sir I hope you are doing well Any update related to Mantel analysis and network. Thanks and regards

On Mon, 5 Feb, 2024, 2:34 pm Muneer Malla, @.***> wrote:

Dear Sir Hope you are fine and doing good Any updates with the datasets Thanks and Regards

On Sun, 4 Feb 2024 at 09:02, Muneer Malla @.***> wrote:

Hi Sir Please find, and once done, Please mention the steps that are needed for future reference Kindly also suggest how to plot individual networks, I compared the networks, but now, How to plot them Thanks and Regards

On Sun, 4 Feb 2024 at 08:09, Chi Liu @.***> wrote:

Please provide the data d1 and d2 ( https://chiliubio.github.io/microeco_tutorial/notes.html#save-function). I will have a try.

— Reply to this email directly, view it on GitHub https://github.com/ChiLiubio/microeco_tutorial/issues/13#issuecomment-1925557609, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASJLNJIJLVVWST6HM6C7KGLYR3YHXAVCNFSM6AAAAAA4DO47CWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMRVGU2TONRQHE . You are receiving this because you authored the thread.Message ID: @.***>

-- With Kind Regards Dr. Muneer Ahmad Malla Postdoctoral Researcher Institute for Water and Wastewater Technology, Durban University of Technology, Durban, (4001) S.A E.mail: @.> @. @.** Phone:+91-9622790800 Scopus Id: 57202376797 Orcid account: https://orcid.org/0000-0001-7878-6240 Google Scholar Account:* https://scholar.google.com/citations?user=hKIujOEAAAAJ&hl=en

-- With Kind Regards Dr. Muneer Ahmad Malla E.mail: @.> @. Phone:+91-9622790800 Scopus Id: 57202376797 Orcid account: https://orcid.org/0000-0001-7878-6240 Google Scholar Account: https://scholar.google.com/citations?user=hKIujOEAAAAJ&hl=en

[ChiLiubio]

Hi. Please donot use by_group = FALSE. The default is NULL, not FALSE. Then it is ok.

t1 <- trans_env$new(dataset = d1, env_cols = 5:10)
t1$cal_mantel(use_measure = "bray", partial_mantel = TRUE)
t2 <- trans_env$new(dataset = d2, env_cols = 5:10)
t2$cal_mantel(use_measure = "bray", partial_mantel = TRUE)

[Muneer111]

Dear Sir Thank You so much, I tried but I am getting the same image. That I previously plotted. What my query is : instead of bacterial groups such as proteobacteria and bacteroidaetes,. I want to use group here, such as SW and PS.

This is the image I got

[image: image.png]

instead I want it this way [image: image.png] Kindly guide me in that direction. Next

And again I created individual networks, but How to plot them

On Sat, 10 Feb 2024 at 10:16, Chi Liu @.***> wrote:

Hi. Please donot use by_group = FALSE. The default is NULL, not FALSE. Then it is ok.

t1 <- trans_env$new(dataset = d1, env_cols = 5:10) t1$cal_mantel(use_measure = "bray", partial_mantel = TRUE) t2 <- trans_env$new(dataset = d2, env_cols = 5:10) t2$cal_mantel(use_measure = "bray", partial_mantel = TRUE)

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-- With Kind Regards Dr. Muneer Ahmad Malla E.mail: @.> @. Phone:+91-9622790800 Scopus Id: 57202376797 Orcid account: https://orcid.org/0000-0001-7878-6240 Google Scholar Account: https://scholar.google.com/citations?user=hKIujOEAAAAJ&hl=en

[Muneer111]

Dear sir Trust you are doing well A gentle reminder about the email I forwarded to you I am again getting the issue. Thanks and Regards

On Sun, 11 Feb, 2024, 11:01 am Muneer Malla, @.***> wrote:

Dear Sir Thank You so much, I tried but I am getting the same image. That I previously plotted. What my query is : instead of bacterial groups such as proteobacteria and bacteroidaetes,. I want to use group here, such as SW and PS.

This is the image I got

[image: image.png]

instead I want it this way [image: image.png] Kindly guide me in that direction. Next

And again I created individual networks, but How to plot them

On Sat, 10 Feb 2024 at 10:16, Chi Liu @.***> wrote:

Hi. Please donot use by_group = FALSE. The default is NULL, not FALSE. Then it is ok.

t1 <- trans_env$new(dataset = d1, env_cols = 5:10) t1$cal_mantel(use_measure = "bray", partial_mantel = TRUE) t2 <- trans_env$new(dataset = d2, env_cols = 5:10) t2$cal_mantel(use_measure = "bray", partial_mantel = TRUE)

— Reply to this email directly, view it on GitHub https://github.com/ChiLiubio/microeco_tutorial/issues/13#issuecomment-1936862614, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASJLNJMJGIM5HSGALL6MI23YS33STAVCNFSM6AAAAAA4DO47CWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMZWHA3DENRRGQ . You are receiving this because you authored the thread.Message ID: @.***>

-- With Kind Regards Dr. Muneer Ahmad Malla E.mail: @.> @. Phone:+91-9622790800 Scopus Id: 57202376797 Orcid account: https://orcid.org/0000-0001-7878-6240 Google Scholar Account: https://scholar.google.com/citations?user=hKIujOEAAAAJ&hl=en

[ChiLiubio]

Please use these steps to extract the microtable object for samples in one group. Then it is same to perform the analysis.

[ChiLiubio]

[Muneer111]

Dear sir Thank you for your response Sorry to disturb again What about Mantel analysis, I don't want Phylum instead I need samples groups like plastisphere and surface water there. As I have attached a figure for your reference. Thanks and regards

On Tue, 13 Feb, 2024, 5:21 am Chi Liu, @.***> wrote:

1707794464843.jpg (view on web) https://github.com/ChiLiubio/microeco_tutorial/assets/20815519/dad67821-17fc-4c87-b936-508b55473949

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[Muneer111]

Hi Sir Kindly please have a look at the issue. Thank you

On Tue, 13 Feb 2024 at 09:12, Muneer Malla @.***> wrote:

Dear sir Thank you for your response Sorry to disturb again What about Mantel analysis, I don't want Phylum instead I need samples groups like plastisphere and surface water there. As I have attached a figure for your reference. Thanks and regards

On Tue, 13 Feb, 2024, 5:21 am Chi Liu, @.***> wrote:

1707794464843.jpg (view on web) https://github.com/ChiLiubio/microeco_tutorial/assets/20815519/dad67821-17fc-4c87-b936-508b55473949

— Reply to this email directly, view it on GitHub https://github.com/ChiLiubio/microeco_tutorial/issues/13#issuecomment-1940361702, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASJLNJOLBDWTCKGNWKXSAYDYTLL4PAVCNFSM6AAAAAA4DO47CWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNBQGM3DCNZQGI . You are receiving this because you authored the thread.Message ID: @.***>

-- With Kind Regards Dr. Muneer Ahmad Malla E.mail: @.> @. Phone:+91-9622790800 Scopus Id: 57202376797 Orcid account: https://orcid.org/0000-0001-7878-6240 Google Scholar Account: https://scholar.google.com/citations?user=hKIujOEAAAAJ&hl=en

[Muneer111]

Dear Sir I hope you are fine and doing well Sorry to disturb you again and again But I am waiting for your response, related the Mantel analysis, I don't wnt to evaluate the analysis with bacterial groups; rather, I want to use groups (like plastisphere and water) in place of bacterial groups and then perform the mantel analysis Like here in this figure Please guide thanks and regards

On Wed, 14 Feb 2024 at 12:59, Muneer Malla @.***> wrote:

Hi Sir Kindly please have a look at the issue. Thank you

On Tue, 13 Feb 2024 at 09:12, Muneer Malla @.***> wrote:

Dear sir Thank you for your response Sorry to disturb again What about Mantel analysis, I don't want Phylum instead I need samples groups like plastisphere and surface water there. As I have attached a figure for your reference. Thanks and regards

On Tue, 13 Feb, 2024, 5:21 am Chi Liu, @.***> wrote:

1707794464843.jpg (view on web) https://github.com/ChiLiubio/microeco_tutorial/assets/20815519/dad67821-17fc-4c87-b936-508b55473949

— Reply to this email directly, view it on GitHub https://github.com/ChiLiubio/microeco_tutorial/issues/13#issuecomment-1940361702, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASJLNJOLBDWTCKGNWKXSAYDYTLL4PAVCNFSM6AAAAAA4DO47CWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNBQGM3DCNZQGI . You are receiving this because you authored the thread.Message ID: @.***>

-- With Kind Regards Dr. Muneer Ahmad Malla E.mail: @.> @. Phone:+91-9622790800 Scopus Id: 57202376797 Orcid account: https://orcid.org/0000-0001-7878-6240 Google Scholar Account: https://scholar.google.com/citations?user=hKIujOEAAAAJ&hl=en

-- With Kind Regards Dr. Muneer Ahmad Malla E.mail: @.> @. Phone:+91-9622790800 Scopus Id: 57202376797 Orcid account: https://orcid.org/0000-0001-7878-6240 Google Scholar Account: https://scholar.google.com/citations?user=hKIujOEAAAAJ&hl=en

[ChiLiubio]

Hi. Please use the following steps to extract samples for a specific group. Then it is same to perform the mantel analysis. Please list the specifici issue that I can reproduce.

[Muneer111]

Dear Sir Thank you so much for your advice and help throughout. I am done with the Mantel analysis. Now I want to plot separate networks between the plastisphere and water. Kindly guide me in this regard. Thanks and regards

On Thu, 15 Feb 2024 at 12:11, Chi Liu @.***> wrote:

Hi. Please use the following steps to extract samples for a specific group. Then it is same to perform the mantel analysis. Please list the specifici issue that I can reproduce. 304285191-dad67821-17fc-4c87-b936-508b55473949.png (view on web) https://github.com/ChiLiubio/microeco_tutorial/assets/20815519/0058d712-50a5-4491-a200-bb3ea8efa0fe

— Reply to this email directly, view it on GitHub https://github.com/ChiLiubio/microeco_tutorial/issues/13#issuecomment-1945456753, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASJLNJLZ22OTPRVJJ2CHK2TYTWUYFAVCNFSM6AAAAAA4DO47CWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNBVGQ2TMNZVGM . You are receiving this because you authored the thread.Message ID: @.***>

-- With Kind Regards Dr. Muneer Ahmad Malla E.mail: @.> @. Phone:+91-9622790800 Scopus Id: 57202376797 Orcid account: https://orcid.org/0000-0001-7878-6240 Google Scholar Account: https://scholar.google.com/citations?user=hKIujOEAAAAJ&hl=en

[Muneer111]

Hi again Dear Sir I am getting this error t1 <- trans_env$new(dataset = tmp1, env_cols = 5:10) Runs successfully t1$cal_mantel(use_measure = "bray", partial_mantel = TRUE)

The beta_diversity in dataset is NULL; try to calculate it ... Error in t2$cal_mantel(use_measure = "bray", partial_mantel = TRUE, by_group = NULL) : attempt to apply non-function

please suggest Thanks and regards

On Sat, 17 Feb 2024 at 21:03, Muneer Malla @.***> wrote:

Dear Sir Thank you so much for your advice and help throughout. I am done with the Mantel analysis. Now I want to plot separate networks between the plastisphere and water. Kindly guide me in this regard. Thanks and regards

On Thu, 15 Feb 2024 at 12:11, Chi Liu @.***> wrote:

Hi. Please use the following steps to extract samples for a specific group. Then it is same to perform the mantel analysis. Please list the specifici issue that I can reproduce. 304285191-dad67821-17fc-4c87-b936-508b55473949.png (view on web) https://github.com/ChiLiubio/microeco_tutorial/assets/20815519/0058d712-50a5-4491-a200-bb3ea8efa0fe

— Reply to this email directly, view it on GitHub https://github.com/ChiLiubio/microeco_tutorial/issues/13#issuecomment-1945456753, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASJLNJLZ22OTPRVJJ2CHK2TYTWUYFAVCNFSM6AAAAAA4DO47CWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNBVGQ2TMNZVGM . You are receiving this because you authored the thread.Message ID: @.***>

-- With Kind Regards Dr. Muneer Ahmad Malla E.mail: @.> @. Phone:+91-9622790800 Scopus Id: 57202376797 Orcid account: https://orcid.org/0000-0001-7878-6240 Google Scholar Account: https://scholar.google.com/citations?user=hKIujOEAAAAJ&hl=en

-- With Kind Regards Dr. Muneer Ahmad Malla E.mail: @.> @. Phone:+91-9622790800 Scopus Id: 57202376797 Orcid account: https://orcid.org/0000-0001-7878-6240 Google Scholar Account: https://scholar.google.com/citations?user=hKIujOEAAAAJ&hl=en

[Muneer111]

Hi Dear Sir Please update about the above mentioned error/ Thanks and Regards

On Sat, 17 Feb 2024 at 22:56, Muneer Malla @.***> wrote:

Hi again Dear Sir I am getting this error t1 <- trans_env$new(dataset = tmp1, env_cols = 5:10) Runs successfully t1$cal_mantel(use_measure = "bray", partial_mantel = TRUE)

The beta_diversity in dataset is NULL; try to calculate it ... Error in t2$cal_mantel(use_measure = "bray", partial_mantel = TRUE, by_group = NULL) : attempt to apply non-function

please suggest Thanks and regards

On Sat, 17 Feb 2024 at 21:03, Muneer Malla @.***> wrote:

Dear Sir Thank you so much for your advice and help throughout. I am done with the Mantel analysis. Now I want to plot separate networks between the plastisphere and water. Kindly guide me in this regard. Thanks and regards

On Thu, 15 Feb 2024 at 12:11, Chi Liu @.***> wrote:

Hi. Please use the following steps to extract samples for a specific group. Then it is same to perform the mantel analysis. Please list the specifici issue that I can reproduce. 304285191-dad67821-17fc-4c87-b936-508b55473949.png (view on web) https://github.com/ChiLiubio/microeco_tutorial/assets/20815519/0058d712-50a5-4491-a200-bb3ea8efa0fe

— Reply to this email directly, view it on GitHub https://github.com/ChiLiubio/microeco_tutorial/issues/13#issuecomment-1945456753, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASJLNJLZ22OTPRVJJ2CHK2TYTWUYFAVCNFSM6AAAAAA4DO47CWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNBVGQ2TMNZVGM . You are receiving this because you authored the thread.Message ID: @.***>

-- With Kind Regards Dr. Muneer Ahmad Malla E.mail: @.> @. Phone:+91-9622790800 Scopus Id: 57202376797 Orcid account: https://orcid.org/0000-0001-7878-6240 Google Scholar Account: https://scholar.google.com/citations?user=hKIujOEAAAAJ&hl=en

-- With Kind Regards Dr. Muneer Ahmad Malla E.mail: @.> @. Phone:+91-9622790800 Scopus Id: 57202376797 Orcid account: https://orcid.org/0000-0001-7878-6240 Google Scholar Account: https://scholar.google.com/citations?user=hKIujOEAAAAJ&hl=en

-- With Kind Regards Dr. Muneer Ahmad Malla E.mail: @.> @. Phone:+91-9622790800 Scopus Id: 57202376797 Orcid account: https://orcid.org/0000-0001-7878-6240 Google Scholar Account: https://scholar.google.com/citations?user=hKIujOEAAAAJ&hl=en

[Muneer111]

Dear Sir Hope you are fine and doing well. Sorry to disturb again Please help out regarding the above error Thanks and Regards

On Mon, 19 Feb, 2024, 9:54 am Muneer Malla, @.***> wrote:

Hi Dear Sir Please update about the above mentioned error/ Thanks and Regards

On Sat, 17 Feb 2024 at 22:56, Muneer Malla @.***> wrote:

Hi again Dear Sir I am getting this error t1 <- trans_env$new(dataset = tmp1, env_cols = 5:10) Runs successfully t1$cal_mantel(use_measure = "bray", partial_mantel = TRUE)

The beta_diversity in dataset is NULL; try to calculate it ... Error in t2$cal_mantel(use_measure = "bray", partial_mantel = TRUE, by_group = NULL) : attempt to apply non-function

please suggest Thanks and regards

On Sat, 17 Feb 2024 at 21:03, Muneer Malla @.***> wrote:

Dear Sir Thank you so much for your advice and help throughout. I am done with the Mantel analysis. Now I want to plot separate networks between the plastisphere and water. Kindly guide me in this regard. Thanks and regards

On Thu, 15 Feb 2024 at 12:11, Chi Liu @.***> wrote:

Hi. Please use the following steps to extract samples for a specific group. Then it is same to perform the mantel analysis. Please list the specifici issue that I can reproduce. 304285191-dad67821-17fc-4c87-b936-508b55473949.png (view on web) https://github.com/ChiLiubio/microeco_tutorial/assets/20815519/0058d712-50a5-4491-a200-bb3ea8efa0fe

— Reply to this email directly, view it on GitHub https://github.com/ChiLiubio/microeco_tutorial/issues/13#issuecomment-1945456753, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASJLNJLZ22OTPRVJJ2CHK2TYTWUYFAVCNFSM6AAAAAA4DO47CWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNBVGQ2TMNZVGM . You are receiving this because you authored the thread.Message ID: @.***>

-- With Kind Regards Dr. Muneer Ahmad Malla E.mail: @.> @. Phone:+91-9622790800 Scopus Id: 57202376797 Orcid account: https://orcid.org/0000-0001-7878-6240 Google Scholar Account: https://scholar.google.com/citations?user=hKIujOEAAAAJ&hl=en

-- With Kind Regards Dr. Muneer Ahmad Malla E.mail: @.> @. Phone:+91-9622790800 Scopus Id: 57202376797 Orcid account: https://orcid.org/0000-0001-7878-6240 Google Scholar Account: https://scholar.google.com/citations?user=hKIujOEAAAAJ&hl=en

-- With Kind Regards Dr. Muneer Ahmad Malla E.mail: @.> @. Phone:+91-9622790800 Scopus Id: 57202376797 Orcid account: https://orcid.org/0000-0001-7878-6240 Google Scholar Account: https://scholar.google.com/citations?user=hKIujOEAAAAJ&hl=en

[Muneer111]

Dear Sir Trust you are doing well Please have a look at the issue that I have got. t1 <- trans_env$new(dataset = tmp1, env_cols = 5:10) Runs successfully

t1$cal_mantel(use_measure = "bray", partial_mantel = TRUE)

The beta_diversity in dataset is NULL; try to calculate it ... Error in t2$cal_mantel(use_measure = "bray", partial_mantel = TRUE, by_group = NULL) : attempt to apply non-function

please suggest Thanks and regards

On Mon, 19 Feb, 2024, 6:50 pm Muneer Malla, @.***> wrote:

Dear Sir Hope you are fine and doing well. Sorry to disturb again Please help out regarding the above error Thanks and Regards

On Mon, 19 Feb, 2024, 9:54 am Muneer Malla, @.***> wrote:

Hi Dear Sir Please update about the above mentioned error/ Thanks and Regards

On Sat, 17 Feb 2024 at 22:56, Muneer Malla @.***> wrote:

Hi again Dear Sir I am getting this error t1 <- trans_env$new(dataset = tmp1, env_cols = 5:10) Runs successfully t1$cal_mantel(use_measure = "bray", partial_mantel = TRUE)

The beta_diversity in dataset is NULL; try to calculate it ... Error in t2$cal_mantel(use_measure = "bray", partial_mantel = TRUE, by_group = NULL) : attempt to apply non-function

please suggest Thanks and regards

On Sat, 17 Feb 2024 at 21:03, Muneer Malla @.***> wrote:

Dear Sir Thank you so much for your advice and help throughout. I am done with the Mantel analysis. Now I want to plot separate networks between the plastisphere and water. Kindly guide me in this regard. Thanks and regards

On Thu, 15 Feb 2024 at 12:11, Chi Liu @.***> wrote:

Hi. Please use the following steps to extract samples for a specific group. Then it is same to perform the mantel analysis. Please list the specifici issue that I can reproduce. 304285191-dad67821-17fc-4c87-b936-508b55473949.png (view on web) https://github.com/ChiLiubio/microeco_tutorial/assets/20815519/0058d712-50a5-4491-a200-bb3ea8efa0fe

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[ChiLiubio]

Please check that how is the t2 generated. I only see the t1 object created by the trans_env class.

[Muneer111]

Hi Professor Hope you are doing well Thanks a lot for helping out. I am almost done, the only thing that is left is the separate networks analysis for surface water and plastisphere, and the keystone taxa that include. Tried to extract the sample for surface water and plastishere but then how to proceed. Please share and suggest.

On Wed, 21 Feb 2024 at 03:41, Chi Liu @.***> wrote:

Please check that how is the t2 generated. I only see the t1 object created by the trans_env class.

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[ChiLiubio]

Hi. The trans_network part (https://chiliubio.github.io/microeco_tutorial/model-based-class.html#trans_network-class) and meconetcomp part (https://chiliubio.github.io/microeco_tutorial/meconetcomp-package.html) both has examples related with the extraction of sample specified subnetwork and properties performance. If these are not enough, could you please provide a toy example to show your aim.

[Muneer111]

Thanks again Professor I want network like this, with key stone species as well Please guide

On Wed, 3 Apr 2024 at 03:07, Chi Liu @.***> wrote:

Hi. The trans_network part ( https://chiliubio.github.io/microeco_tutorial/model-based-class.html#trans_network-class) and meconetcomp part ( https://chiliubio.github.io/microeco_tutorial/meconetcomp-package.html) both has examples related with the extraction of sample specified subnetwork and properties performance. If these are not enough, could you please provide a toy example to show your aim.

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-- With Kind Regards Dr. Muneer Ahmad Malla E.mail: @.> @. Phone:+91-9622790800 Scopus Id: 57202376797 Orcid account: https://orcid.org/0000-0001-7878-6240 Google Scholar Account: https://scholar.google.com/citations?user=hKIujOEAAAAJ&hl=en

[Muneer111]

Hi Professor Hope you are doing well Please find the network analysis above. This type of analysis I need. Please suggest Thanks

On Wed, 3 Apr, 2024, 11:23 am Muneer Malla, @.***> wrote:

Thanks again Professor I want network like this, with key stone species as well Please guide

On Wed, 3 Apr 2024 at 03:07, Chi Liu @.***> wrote:

Hi. The trans_network part ( https://chiliubio.github.io/microeco_tutorial/model-based-class.html#trans_network-class) and meconetcomp part ( https://chiliubio.github.io/microeco_tutorial/meconetcomp-package.html) both has examples related with the extraction of sample specified subnetwork and properties performance. If these are not enough, could you please provide a toy example to show your aim.

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-- With Kind Regards Dr. Muneer Ahmad Malla E.mail: @.> @. Phone:+91-9622790800 Scopus Id: 57202376797 Orcid account: https://orcid.org/0000-0001-7878-6240 Google Scholar Account: https://scholar.google.com/citations?user=hKIujOEAAAAJ&hl=en

[Muneer111]

Hi Professor Hope you are doing well A gentle reminder regarding the network analysis Thanks and regards

On Fri, 5 Apr, 2024, 12:26 am Muneer Malla, @.***> wrote:

Hi Professor Hope you are doing well Please find the network analysis above. This type of analysis I need. Please suggest Thanks

On Wed, 3 Apr, 2024, 11:23 am Muneer Malla, @.***> wrote:

Thanks again Professor I want network like this, with key stone species as well Please guide

On Wed, 3 Apr 2024 at 03:07, Chi Liu @.***> wrote:

Hi. The trans_network part ( https://chiliubio.github.io/microeco_tutorial/model-based-class.html#trans_network-class) and meconetcomp part ( https://chiliubio.github.io/microeco_tutorial/meconetcomp-package.html) both has examples related with the extraction of sample specified subnetwork and properties performance. If these are not enough, could you please provide a toy example to show your aim.

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-- With Kind Regards Dr. Muneer Ahmad Malla E.mail: @.> @. Phone:+91-9622790800 Scopus Id: 57202376797 Orcid account: https://orcid.org/0000-0001-7878-6240 Google Scholar Account: https://scholar.google.com/citations?user=hKIujOEAAAAJ&hl=en

[Muneer111]

Hi Professor again Just a gentle reminder related to network analysis. Thanks and regards

On Mon, 8 Apr, 2024, 4:13 am Muneer Malla, @.***> wrote:

Hi Professor Hope you are doing well A gentle reminder regarding the network analysis Thanks and regards

On Fri, 5 Apr, 2024, 12:26 am Muneer Malla, @.***> wrote:

Hi Professor Hope you are doing well Please find the network analysis above. This type of analysis I need. Please suggest Thanks

On Wed, 3 Apr, 2024, 11:23 am Muneer Malla, @.***> wrote:

Thanks again Professor I want network like this, with key stone species as well Please guide

On Wed, 3 Apr 2024 at 03:07, Chi Liu @.***> wrote:

Hi. The trans_network part ( https://chiliubio.github.io/microeco_tutorial/model-based-class.html#trans_network-class) and meconetcomp part ( https://chiliubio.github.io/microeco_tutorial/meconetcomp-package.html) both has examples related with the extraction of sample specified subnetwork and properties performance. If these are not enough, could you please provide a toy example to show your aim.

— Reply to this email directly, view it on GitHub https://github.com/ChiLiubio/microeco_tutorial/issues/13#issuecomment-2033361105, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASJLNJLJAHKWHEPORCQIYZTY3NI5VAVCNFSM6AAAAAA4DO47CWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMZTGM3DCMJQGU . You are receiving this because you authored the thread.Message ID: @.***>

-- With Kind Regards Dr. Muneer Ahmad Malla E.mail: @.> @. Phone:+91-9622790800 Scopus Id: 57202376797 Orcid account: https://orcid.org/0000-0001-7878-6240 Google Scholar Account: https://scholar.google.com/citations?user=hKIujOEAAAAJ&hl=en

[Muneer111]

Dear Prof Hope you are keeping well I am waiting for your response related to network analysis. As in my previous email, I have uploaded a toy example of how I want the networks for my data. Kindly please help and suggest Thanks and Regards

On Tue, 9 Apr, 2024, 4:51 am Muneer Malla, @.***> wrote:

Hi Professor again Just a gentle reminder related to network analysis. Thanks and regards

On Mon, 8 Apr, 2024, 4:13 am Muneer Malla, @.***> wrote:

Hi Professor Hope you are doing well A gentle reminder regarding the network analysis Thanks and regards

On Fri, 5 Apr, 2024, 12:26 am Muneer Malla, @.***> wrote:

Hi Professor Hope you are doing well Please find the network analysis above. This type of analysis I need. Please suggest Thanks

On Wed, 3 Apr, 2024, 11:23 am Muneer Malla, @.***> wrote:

Thanks again Professor I want network like this, with key stone species as well Please guide

On Wed, 3 Apr 2024 at 03:07, Chi Liu @.***> wrote:

Hi. The trans_network part ( https://chiliubio.github.io/microeco_tutorial/model-based-class.html#trans_network-class) and meconetcomp part ( https://chiliubio.github.io/microeco_tutorial/meconetcomp-package.html) both has examples related with the extraction of sample specified subnetwork and properties performance. If these are not enough, could you please provide a toy example to show your aim.

— Reply to this email directly, view it on GitHub https://github.com/ChiLiubio/microeco_tutorial/issues/13#issuecomment-2033361105, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASJLNJLJAHKWHEPORCQIYZTY3NI5VAVCNFSM6AAAAAA4DO47CWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMZTGM3DCMJQGU . You are receiving this because you authored the thread.Message ID: @.***>

-- With Kind Regards Dr. Muneer Ahmad Malla E.mail: @.> @. Phone:+91-9622790800 Scopus Id: 57202376797 Orcid account: https://orcid.org/0000-0001-7878-6240 Google Scholar Account: https://scholar.google.com/citations?user=hKIujOEAAAAJ&hl=en

[Muneer111]

Hi Professor I hope you are doing well, Please do the needful related to network analysis. I have forwarded a toy example showing the networks I need. Thanks

On Fri, 12 Apr, 2024, 7:06 pm Muneer Malla, @.***> wrote:

Dear Prof Hope you are keeping well I am waiting for your response related to network analysis. As in my previous email, I have uploaded a toy example of how I want the networks for my data. Kindly please help and suggest Thanks and Regards

On Tue, 9 Apr, 2024, 4:51 am Muneer Malla, @.***> wrote:

Hi Professor again Just a gentle reminder related to network analysis. Thanks and regards

On Mon, 8 Apr, 2024, 4:13 am Muneer Malla, @.***> wrote:

Hi Professor Hope you are doing well A gentle reminder regarding the network analysis Thanks and regards

On Fri, 5 Apr, 2024, 12:26 am Muneer Malla, @.***> wrote:

Hi Professor Hope you are doing well Please find the network analysis above. This type of analysis I need. Please suggest Thanks

On Wed, 3 Apr, 2024, 11:23 am Muneer Malla, @.***> wrote:

Thanks again Professor I want network like this, with key stone species as well Please guide

On Wed, 3 Apr 2024 at 03:07, Chi Liu @.***> wrote:

Hi. The trans_network part ( https://chiliubio.github.io/microeco_tutorial/model-based-class.html#trans_network-class) and meconetcomp part ( https://chiliubio.github.io/microeco_tutorial/meconetcomp-package.html) both has examples related with the extraction of sample specified subnetwork and properties performance. If these are not enough, could you please provide a toy example to show your aim.

— Reply to this email directly, view it on GitHub https://github.com/ChiLiubio/microeco_tutorial/issues/13#issuecomment-2033361105, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASJLNJLJAHKWHEPORCQIYZTY3NI5VAVCNFSM6AAAAAA4DO47CWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMZTGM3DCMJQGU . You are receiving this because you authored the thread.Message ID: @.***>

-- With Kind Regards Dr. Muneer Ahmad Malla E.mail: @.> @. Phone:+91-9622790800 Scopus Id: 57202376797 Orcid account: https://orcid.org/0000-0001-7878-6240 Google Scholar Account: https://scholar.google.com/citations?user=hKIujOEAAAAJ&hl=en

[Muneer111]

Hi Profesor This is a gentle reminder thanks

On Tue, 16 Apr 2024 at 19:51, Muneer Malla @.***> wrote:

Hi Professor I hope you are doing well, Please do the needful related to network analysis. I have forwarded a toy example showing the networks I need. Thanks

On Fri, 12 Apr, 2024, 7:06 pm Muneer Malla, @.***> wrote:

Dear Prof Hope you are keeping well I am waiting for your response related to network analysis. As in my previous email, I have uploaded a toy example of how I want the networks for my data. Kindly please help and suggest Thanks and Regards

On Tue, 9 Apr, 2024, 4:51 am Muneer Malla, @.***> wrote:

Hi Professor again Just a gentle reminder related to network analysis. Thanks and regards

On Mon, 8 Apr, 2024, 4:13 am Muneer Malla, @.***> wrote:

Hi Professor Hope you are doing well A gentle reminder regarding the network analysis Thanks and regards

On Fri, 5 Apr, 2024, 12:26 am Muneer Malla, @.***> wrote:

Hi Professor Hope you are doing well Please find the network analysis above. This type of analysis I need. Please suggest Thanks

On Wed, 3 Apr, 2024, 11:23 am Muneer Malla, @.***> wrote:

Thanks again Professor I want network like this, with key stone species as well Please guide

On Wed, 3 Apr 2024 at 03:07, Chi Liu @.***> wrote:

Hi. The trans_network part ( https://chiliubio.github.io/microeco_tutorial/model-based-class.html#trans_network-class) and meconetcomp part ( https://chiliubio.github.io/microeco_tutorial/meconetcomp-package.html) both has examples related with the extraction of sample specified subnetwork and properties performance. If these are not enough, could you please provide a toy example to show your aim.

— Reply to this email directly, view it on GitHub https://github.com/ChiLiubio/microeco_tutorial/issues/13#issuecomment-2033361105, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASJLNJLJAHKWHEPORCQIYZTY3NI5VAVCNFSM6AAAAAA4DO47CWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMZTGM3DCMJQGU . You are receiving this because you authored the thread.Message ID: @.***>

-- With Kind Regards Dr. Muneer Ahmad Malla E.mail: @.> @. Phone:+91-9622790800 Scopus Id: 57202376797 Orcid account: https://orcid.org/0000-0001-7878-6240 Google Scholar Account: https://scholar.google.com/citations?user=hKIujOEAAAAJ&hl=en

-- With Kind Regards Dr. Muneer Ahmad Malla E.mail: @.> @. Phone:+91-9622790800 Scopus Id: 57202376797 Orcid account: https://orcid.org/0000-0001-7878-6240 Google Scholar Account: https://scholar.google.com/citations?user=hKIujOEAAAAJ&hl=en