metacoder

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Welcome to the google group for the metacoder R package

You can ask questions, leave comments, or report errors here. If you are reporting an error, consider reporting it as a GitHub issue here. We are interested to hear what people think about the package and how it can be improved so feel free to leave comments or suggestions.

Documentation:
https://grunwaldlab.github.io/metacoder_documentation/

Publication:
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005404

GitHub repository:
https://github.com/grunwaldlab/metacoder

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Laurent Cauquil, … Laurent Cauquil3

10/15/20

Subset of heat_tree_matrix

Ok, thank you for your response. I will try the first option, the reproducible way. Best, Laurent Le

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Subset of heat_tree_matrix

Ok, thank you for your response. I will try the first option, the reproducible way. Best, Laurent Le

10/15/20

MD.Shaminur Rahman

5/5/20

About Pathoscope, library produce an empty files

I am very new in coding. I am trying to use pathoscope but when the library is going to build, there

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About Pathoscope, library produce an empty files

I am very new in coding. I am trying to use pathoscope but when the library is going to build, there

5/5/20

swa...@gmail.com, Zachary Foster8

4/13/20

Trying my hand on a heat_tree_matrix but getting an error

Hi Zachary, Sorry for the late response. Thanks a lot this! I'll get on it after Easter! On

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Trying my hand on a heat_tree_matrix but getting an error

Hi Zachary, Sorry for the late response. Thanks a lot this! I'll get on it after Easter! On

4/13/20

tuffr...@gmail.com, Zachary Foster2

2/26/20

Thanks! If you limit the node labels with node_label_max, it picks the biggest labels. You can show

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Thanks! If you limit the node labels with node_label_max, it picks the biggest labels. You can show

2/26/20

lfca...@gmail.com, Zachary Foster3

11/22/19

Highlight presence/absence OTU in one heat tree for each sample

Ok, I understand, now it's clear Thank you for your quick response, Best, Laurent Le mercredi 20

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Highlight presence/absence OTU in one heat tree for each sample

Ok, I understand, now it's clear Thank you for your quick response, Best, Laurent Le mercredi 20

11/22/19

nieli...@gmail.com, Zachary Foster2

10/28/19

Hello, Take a look at this tutorial and let me know if you still have questions: https://grunwaldlab.

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Hello, Take a look at this tutorial and let me know if you still have questions: https://grunwaldlab.

10/28/19

cle...@gmail.com, Zachary Foster2

7/15/19

could not find function "extract_taxonomy"

Hello Celine, That function was replaced by `parse_tax_data`, which works in a similar way. If you

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could not find function "extract_taxonomy"

Hello Celine, That function was replaced by `parse_tax_data`, which works in a similar way. If you

7/15/19

msis...@gmail.com, Zachary Foster4

6/7/19

Adapting heat trees for non-taxonomic analyses

Hi Matt, Nice! Yea, you can use the `node_color_interval` option for that. Set the max value (the

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Adapting heat trees for non-taxonomic analyses

Hi Matt, Nice! Yea, you can use the `node_color_interval` option for that. Set the max value (the

6/7/19

jordan.e...@uhasselt.be, Zachary Foster3

6/7/19

Deseq2 and Metacoder on metagenomic count data

Hello Jordan, I looked into this and I think I have a solution. The summary is that DESeq2 uses the

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Deseq2 and Metacoder on metagenomic count data

Hello Jordan, I looked into this and I think I have a solution. The summary is that DESeq2 uses the

6/7/19

lfca...@gmail.com, Zachary Foster3

6/5/19

How to correct p-value for multiple comparisons regarding taxonomic rank

Perfect, it does exactly what I wanted. Thank you, Laurent Le mardi 4 juin 2019 20:04:21 UTC+2,

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How to correct p-value for multiple comparisons regarding taxonomic rank

Perfect, it does exactly what I wanted. Thank you, Laurent Le mardi 4 juin 2019 20:04:21 UTC+2,

6/5/19

brandily...@gmail.com, Zachary Foster3

5/31/19

removing taxa with missing names in heat_tree display

Hi Zach, Thanks for the quick response! This was exactly my problem. I'm still learning the

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removing taxa with missing names in heat_tree display

Hi Zach, Thanks for the quick response! This was exactly my problem. I'm still learning the

5/31/19

Xio Lee, … Zachary Foster4

5/15/19

parsing phyloseq obj subscript out of bound error

Hello, Sorry for the error. Can you send my your data or a subset that produces that same error so I

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parsing phyloseq obj subscript out of bound error

Hello, Sorry for the error. Can you send my your data or a subset that produces that same error so I

5/15/19

michael...@gmail.com, Zachary Foster2

4/30/19

Removing legend

Hi Michael, You can use "make_node_legend = FALSE" and "make_edge_legend = FALSE"

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Removing legend

Hi Michael, You can use "make_node_legend = FALSE" and "make_edge_legend = FALSE"

4/30/19

filipam...@gmail.com, Zachary Foster2

3/13/19

Data quality control - filter by otu_props

Hello Filipa, Thanks! Yes, OTU data is usually a table and you can filter a table on any per-row

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Data quality control - filter by otu_props

Hello Filipa, Thanks! Yes, OTU data is usually a table and you can filter a table on any per-row

3/13/19

sonumu...@gmail.com, Zachary Foster2

7/2/18

Metacoder plots for UNITE taxonomy

Hello Sunil, Can you attach a file with a subset of your data? Thanks! Best, Zach

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Metacoder plots for UNITE taxonomy

Hello Sunil, Can you attach a file with a subset of your data? Thanks! Best, Zach

7/2/18

Neelam Redekar, Zachary Foster3

5/30/18

Error with filter_taxa

Interesting, when I try to replicate your error message, I get: > library(taxa) > filter_taxa(

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Error with filter_taxa

Interesting, when I try to replicate your error message, I get: > library(taxa) > filter_taxa(

5/30/18

Denis Kutnjak, Zachary Foster4

4/25/18

Parsing BIOM1 format exported from MEGAN

Thanks Denis! I am glad it worked -Zach

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Parsing BIOM1 format exported from MEGAN

Thanks Denis! I am glad it worked -Zach

4/25/18

juan.a....@gmail.com, Zachary Foster4

3/2/18

One heat tree showing OTUs from two samples in different colours

Hi Juan, You can do that using what we call a differential heat tree. There is an example of how to

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One heat tree showing OTUs from two samples in different colours

Hi Juan, You can do that using what we call a differential heat tree. There is an example of how to

3/2/18

lara.c...@gmail.com, Zachary Foster3

1/10/18

Problem with converting a phyloseq object to a taxmap object

Success!!! Many thanks for you help and fast response! Lara On Tue, Jan 9, 2018 at 7:43 PM, Zachary

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Problem with converting a phyloseq object to a taxmap object

Success!!! Many thanks for you help and fast response! Lara On Tue, Jan 9, 2018 at 7:43 PM, Zachary

1/10/18

sbue...@asu.edu, Zachary Foster3

1/9/18

Taxonomy database in Uniprot format for classification with USEARCH

Zach, thank you so much for your help.. the example file is great to really understand what you did,

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Taxonomy database in Uniprot format for classification with USEARCH

Zach, thank you so much for your help.. the example file is great to really understand what you did,

1/9/18

Richard Rodrigues, Zachary Foster5

1/8/18

Heat tree for QIIME OTU tables

Not yet, I'll try it. Thanks. On Monday, January 8, 2018 at 9:55:20 AM UTC-8, Zachary Foster

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Heat tree for QIIME OTU tables

Not yet, I'll try it. Thanks. On Monday, January 8, 2018 at 9:55:20 AM UTC-8, Zachary Foster

1/8/18

blakem...@gmail.com, Zachary Foster4

1/3/18

In silico PCR primer match sequences

Hello Blake, Sorry for the delay! It was harder than I expected and the holidays slowed things down

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In silico PCR primer match sequences

Hello Blake, Sorry for the delay! It was harder than I expected and the holidays slowed things down

1/3/18

Osnat Limanovich, Zachary Foster7

12/28/17

problem in reading data from a previous tool (Pathoscope)

Thanks Zach! Opening a new session did solve the problem I posted about yesterday, that's good to

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problem in reading data from a previous tool (Pathoscope)

Thanks Zach! Opening a new session did solve the problem I posted about yesterday, that's good to

12/28/17

sanchezarr...@gmail.com, … Zachary Foster7

11/29/17

How to represent OTU abundance in heat trees

Hello Miguel, Thanks for figuring that out! I will look into that. -Zach

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How to represent OTU abundance in heat trees

Hello Miguel, Thanks for figuring that out! I will look into that. -Zach

11/29/17

javie...@gmail.com, Zachary Foster2

11/20/17

export extract_taxonomy object

Hello! The two tables in the object are just data.frames, so you can save them like any other table

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export extract_taxonomy object

Hello! The two tables in the object are just data.frames, so you can save them like any other table

11/20/17

sanchezarr...@gmail.com, Zachary Foster2

10/27/17

Legend of heat maps comparable

Hello! I think setting the "node_size_interval"/"node_color_interval"/"

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Legend of heat maps comparable

Hello! I think setting the "node_size_interval"/"node_color_interval"/"

10/27/17

ladyp...@gmail.com, Zachary Foster2

9/29/17

Using Qiime OTU table as input for metacoder

Hello Joany, There is no dedicated parser for that format, but the new `taxa` package has a parser

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Using Qiime OTU table as input for metacoder

Hello Joany, There is no dedicated parser for that format, but the new `taxa` package has a parser

9/29/17

Jean-Francois Martin, Zachary Foster10

9/20/17

parsing taxonomy from custom format

Hi Jef, I am sorry for the delay! I have a lot of other stuff going on right now and I overlooked

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parsing taxonomy from custom format

Hi Jef, I am sorry for the delay! I have a lot of other stuff going on right now and I overlooked

9/20/17

zifca...@gmail.com, Zachary Foster4

9/7/17

taxonomy table from blast search with metabarcoder

Hi Lucia, I used your script to download the files you downloaded and looked at them. I don't

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taxonomy table from blast search with metabarcoder

Hi Lucia, I used your script to download the files you downloaded and looked at them. I don't

9/7/17

Clarissa B., Zachary Foster2

7/25/17

Using data from previous tool (MGRAST) - input file doubt

Hi Clarissa, Yes, that can be used without much trouble, but with only domain and phylum, it might be

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Using data from previous tool (MGRAST) - input file doubt

Hi Clarissa, Yes, that can be used without much trouble, but with only domain and phylum, it might be

7/25/17

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