Joss branch by grabear · Pull Request #79 · vallenderlab/MicrobiomeR

grabear · 2019-02-19T01:32:48Z

MicrobiomeR 0.5.0

Added the JOSS paper and draft vignette
Changed correlation plots
- Removed color from background
- Removed hard coded plot limits
- Added "1:1" line and Average lines
- Added a trans parameter to transform the x and y axis
Changed function names
- From create_metacoder to create_taxmap
- From agglomerate_metacoder to agglomerate_taxmap
- From melt_metacoder to melt_taxmap
Bugs
- Fixed output_dir bug where error should have been a warning
- Fixed correlation plot bug where treatments were on the wrong axis.
- Fixed output message for heat tree plots.

…ilva)

…o correlation plot function.

…egends, added

sdhutchins · 2019-02-20T18:03:34Z

I'm guessing some parameter is off in the analysis.Rmd vignette after the changes you made. @grabear

grabear · 2019-02-20T18:49:44Z

I'm guessing some parameter is off in the analysis.Rmd vignette after the changes you made. @grabear

Yea.. I was too tired last night, but I may have figured it out. Fingers crossed

grabear · 2019-02-20T19:10:10Z

I forgot to rebuild the package after that last commit. So after I rebuild hopefully things work out.

sdhutchins · 2019-02-20T22:47:42Z

- Session info --------------------------------------------------------------------------------------------------------------------------------------------------------------
 setting  value                       
 version  R version 3.5.1 (2018-07-02)
 os       Windows 7 x64 SP 1          
 system   x86_64, mingw32             
 ui       RStudio                     
 language (EN)                        
 collate  English_United States.1252  
 ctype    English_United States.1252  
 tz       America/Chicago             
 date     2019-02-20                  

- Packages ------------------------------------------------------------------------------------------------------------------------------------------------------------------
 package      * version    date       lib source                                   
 ade4           1.7-13     2018-08-31 [1] CRAN (R 3.5.1)                           
 ape            5.2        2018-09-24 [1] CRAN (R 3.5.1)                           
 assertthat     0.2.0      2017-04-11 [1] CRAN (R 3.5.1)                           
 backports      1.1.3      2018-12-14 [1] CRAN (R 3.5.1)                           
 Biobase        2.42.0     2018-10-30 [1] Bioconductor                             
 BiocGenerics   0.28.0     2018-10-30 [1] Bioconductor                             
 biomformat     1.10.0     2018-10-30 [1] Bioconductor                             
 Biostrings     2.50.1     2018-11-06 [1] Bioconductor                             
 callr          3.1.1      2018-12-21 [1] CRAN (R 3.5.2)                           
 cli            1.0.1      2018-09-25 [1] CRAN (R 3.5.1)                           
 cluster        2.0.7-1    2018-04-13 [2] CRAN (R 3.5.1)                           
 codetools      0.2-15     2016-10-05 [2] CRAN (R 3.5.1)                           
 colorspace     1.4-0      2019-01-13 [1] CRAN (R 3.5.2)                           
 crayon         1.3.4      2019-01-08 [1] Github (r-lib/crayon@74bee76)            
 curl           3.3        2019-01-10 [1] CRAN (R 3.5.2)                           
 data.table     1.12.0     2019-01-13 [1] CRAN (R 3.5.2)                           
 desc           1.2.0      2018-05-01 [1] CRAN (R 3.5.1)                           
 devtools       2.0.1      2018-10-26 [1] CRAN (R 3.5.1)                           
 digest         0.6.18     2018-10-10 [1] CRAN (R 3.5.1)                           
 diptest        0.75-7     2016-12-05 [1] CRAN (R 3.5.0)                           
 dplyr          0.8.0.1    2019-02-15 [1] CRAN (R 3.5.2)                           
 evaluate       0.13       2019-02-12 [1] CRAN (R 3.5.2)                           
 fansi          0.4.0      2018-10-05 [1] CRAN (R 3.5.1)                           
 forcats        0.4.0      2019-02-17 [1] CRAN (R 3.5.2)                           
 foreach        1.4.4      2017-12-12 [1] CRAN (R 3.5.1)                           
 fs             1.2.6      2018-08-23 [1] CRAN (R 3.5.1)                           
 ggplot2      * 3.1.0      2018-10-25 [1] CRAN (R 3.5.1)                           
 ggpubr       * 0.2.999    2018-12-06 [1] Github (kassambara/ggpubr@de26170)       
 ggrepel        0.8.0      2018-05-09 [1] CRAN (R 3.5.1)                           
 ggsignif       0.5.0      2019-02-20 [1] CRAN (R 3.5.1)                           
 ggthemes       4.1.0      2019-02-19 [1] CRAN (R 3.5.1)                           
 glue           1.3.0.9000 2019-01-26 [1] Github (tidyverse/glue@a1143f7)          
 gridExtra      2.3        2017-09-09 [1] CRAN (R 3.5.1)                           
 gtable         0.2.0      2016-02-26 [1] CRAN (R 3.5.1)                           
 hms            0.4.2      2018-03-10 [1] CRAN (R 3.5.1)                           
 htmltools      0.3.6      2017-04-28 [1] CRAN (R 3.5.1)                           
 httr           1.4.0      2018-12-11 [1] CRAN (R 3.5.2)                           
 igraph         1.2.4      2019-02-13 [1] CRAN (R 3.5.2)                           
 IRanges        2.16.0     2018-10-30 [1] Bioconductor                             
 iterators      1.0.10     2018-07-13 [1] CRAN (R 3.5.1)                           
 jsonlite       1.6        2018-12-07 [1] CRAN (R 3.5.1)                           
 kableExtra     1.0.1      2019-01-22 [1] CRAN (R 3.5.2)                           
 knitr          1.21       2018-12-10 [1] CRAN (R 3.5.1)                           
 labeling       0.3        2014-08-23 [1] CRAN (R 3.5.0)                           
 lattice        0.20-35    2017-03-25 [2] CRAN (R 3.5.1)                           
 lazyeval       0.2.1      2017-10-29 [1] CRAN (R 3.5.1)                           
 magrittr     * 1.5        2014-11-22 [1] CRAN (R 3.5.1)                           
 MASS           7.3-50     2018-04-30 [2] CRAN (R 3.5.1)                           
 Matrix         1.2-14     2018-04-13 [2] CRAN (R 3.5.1)                           
 memoise        1.1.0      2017-04-21 [1] CRAN (R 3.5.1)                           
 metacoder      0.3.1      2019-01-04 [1] CRAN (R 3.5.2)                           
 mgcv           1.8-24     2018-06-23 [2] CRAN (R 3.5.1)                           
 microbiome     1.5.27     2019-02-11 [1] Github (microbiome/microbiome@db93d7a)   
 MicrobiomeR  * 0.4.1      2019-02-20 [1] Github (vallenderlab/MicrobiomeR@095a03c)
 modes          0.7.0      2016-03-07 [1] CRAN (R 3.5.0)                           
 multtest       2.38.0     2018-10-30 [1] Bioconductor                             
 munsell        0.5.0      2018-06-12 [1] CRAN (R 3.5.1)                           
 nlme           3.1-137    2018-04-07 [2] CRAN (R 3.5.1)                           
 permute        0.9-4      2016-09-09 [1] CRAN (R 3.5.1)                           
 phyloseq     * 1.25.2     2018-12-03 [1] Github (joey711/phyloseq@cd7da46)        
 pillar         1.3.1      2018-12-15 [1] CRAN (R 3.5.1)                           
 pkgbuild       1.0.2      2018-10-16 [1] CRAN (R 3.5.1)                           
 pkgconfig      2.0.2      2018-08-16 [1] CRAN (R 3.5.1)                           
 pkgload        1.0.2      2018-10-29 [1] CRAN (R 3.5.1)                           
 plyr           1.8.4      2016-06-08 [1] CRAN (R 3.5.1)                           
 prettyunits    1.0.2      2015-07-13 [1] CRAN (R 3.5.1)                           
 processx       3.2.1      2018-12-05 [1] CRAN (R 3.5.1)                           
 ps             1.3.0      2018-12-21 [1] CRAN (R 3.5.2)                           
 purrr          0.3.0      2019-01-27 [1] CRAN (R 3.5.2)                           
 R6             2.4.0      2019-02-14 [1] CRAN (R 3.5.2)                           
 Rcpp           1.0.0      2018-11-07 [1] CRAN (R 3.5.1)                           
 readr          1.3.1      2018-12-21 [1] CRAN (R 3.5.2)                           
 remotes        2.0.2      2018-10-30 [1] CRAN (R 3.5.1)                           
 reshape2       1.4.3      2017-12-11 [1] CRAN (R 3.5.1)                           
 rhdf5          2.26.0     2018-10-30 [1] Bioconductor                             
 Rhdf5lib       1.4.1      2018-11-22 [1] Bioconductor                             
 rlang          0.3.1      2019-01-08 [1] CRAN (R 3.5.1)                           
 rmarkdown      1.11       2018-12-08 [1] CRAN (R 3.5.1)                           
 rprojroot      1.3-2      2018-01-03 [1] CRAN (R 3.5.1)                           
 rstudioapi     0.9.0      2019-01-12 [1] Github (rstudio/rstudioapi@aa6cdb0)      
 Rtsne          0.15       2018-11-10 [1] CRAN (R 3.5.1)                           
 rvest          0.3.2      2016-06-17 [1] CRAN (R 3.5.1)                           
 S4Vectors      0.20.1     2018-11-09 [1] Bioconductor                             
 scales         1.0.0      2018-08-09 [1] CRAN (R 3.5.1)                           
 scico          1.1.0      2018-11-20 [1] CRAN (R 3.5.1)                           
 sessioninfo    1.1.1      2018-11-05 [1] CRAN (R 3.5.1)                           
 shades       * 1.3.1      2019-02-12 [1] Github (jonclayden/shades@b1ac3e5)       
 stringi        1.3.1      2019-02-13 [1] CRAN (R 3.5.2)                           
 stringr        1.4.0      2019-02-10 [1] CRAN (R 3.5.2)                           
 survival       2.42-3     2018-04-16 [2] CRAN (R 3.5.1)                           
 taxa           0.3.2      2019-01-02 [1] CRAN (R 3.5.1)                           
 testthat       2.0.1      2018-10-13 [1] CRAN (R 3.5.1)                           
 tibble         2.0.1      2019-01-12 [1] CRAN (R 3.5.2)                           
 tidyr          0.8.2      2018-10-28 [1] CRAN (R 3.5.1)                           
 tidyselect     0.2.5      2018-10-11 [1] CRAN (R 3.5.1)                           
 usethis        1.4.0      2018-08-14 [1] CRAN (R 3.5.1)                           
 utf8           1.1.4      2018-05-24 [1] CRAN (R 3.5.1)                           
 vegan          2.5-4      2019-02-04 [1] CRAN (R 3.5.2)                           
 viridis        0.5.1      2018-03-29 [1] CRAN (R 3.5.1)                           
 viridisLite    0.3.0      2018-02-01 [1] CRAN (R 3.5.1)                           
 webshot        0.5.1      2018-09-28 [1] CRAN (R 3.5.1)                           
 withr          2.1.2      2018-03-15 [1] CRAN (R 3.5.1)                           
 xfun           0.4        2018-10-23 [1] CRAN (R 3.5.1)                           
 xml2           1.2.0      2018-01-24 [1] CRAN (R 3.5.1)                           
 XVector        0.22.0     2018-10-30 [1] Bioconductor                             
 zlibbioc       1.28.0     2018-10-30 [1] Bioconductor                             

[1] C:/Users/shutchins2/Documents/R/win-library/3.5
[2] C:/Program Files/R/R-3.5.1/library

grabear · 2019-02-21T04:06:40Z

@sdhutchins Thoughts?

sdhutchins · 2019-02-21T06:28:17Z

After your tweet, it may be best to find whatever bug was introduced by dplyr.

grabear · 2019-02-21T15:22:15Z

dplyr also relies on the new (Feb 4th) purr 0.3.0

grabear · 2019-02-21T15:23:04Z

tidyverse/googlesheets4@e0f9eca

grabear · 2019-02-21T15:23:37Z

Not sure if that's significant

…omeR into joss-branch

grabear · 2019-02-26T17:27:58Z

I'm going to resolve the conflicts introduced from #83 and then try to merge. I will also rebuild the docs @sdhutchins

grabear · 2019-02-26T17:46:39Z

Closing this branch to fix conflicts and to update the paper.

grabear and others added 21 commits January 24, 2019 12:50

Initial commit of joss paper files.

944d9cb

Changed create_metacoder to create_taxmap.

4f5a590

Fixed any reference of "metacoder object" to "taxmap object".

46ccb94

Changed agglomerate_metacoder to agglomerate_taxmap.

ad9c474

Changed melt_metacoder to melt_taxmap.

b4161ab

Bumped the version and added NEWS.

5472835

Added a tab for the paper.

7c103f3

Added references to the bib file (phyloseq, metacoder, taxa, qiime, s…

bcba410

…ilva)

Removed unnecessary dependency.

0dda527

Created a tab in the pkgdown navbar for the publication.

da893ab

Fixed a bug in the output_dir function.

883eda5

Removed bg color/dotted lines, and added a transformation parameter t…

1e46d99

…o correlation plot function.

Added functionality to edit title including the title parameter

c08ed3a

Fixed bug where treatments are placed in the wrong axis. Added line l…

98a8b58

…egends, added

Fixed output message for heat-tree plots

bdbd73e

Updated version and added correlation plot changes and bugs.

6578f20

Updated the paper and related documents.

921c4c2

Added a draft of the publication to the vignettes.

da4f3df

Changed Reference tab to Functions tab.

8cef5b3

Updated package/pkgdown after build and install

14181b7

Updated news line.

26bbc4b

grabear added Status: Review Needed 👁️ 👁️ Type: Bug 🪲 🪲 🪲 🪲 Priority: Critical 🔥🔥🔥🔥 Type: Maintenance 🔧 Type: Enhancement ❤️ Type: Documentation 📄 labels Feb 19, 2019

grabear assigned grabear and sdhutchins Feb 19, 2019

grabear requested a review from sdhutchins February 19, 2019 01:32

grabear and others added 3 commits February 19, 2019 20:22

Updated package after build-check and fixes

ffd3ed4

Updated pkgdown docs

6bff22f

Updated NEWS

67b85e2

Potential travis-ci fix.

9ae1404

Updated namespace after package build.

b937108

grabear mentioned this pull request Feb 20, 2019

WIP Joss debug branch #82

Closed

grabear and others added 3 commits February 20, 2019 19:07

Updated travis config

6843324

Fixed duplicate vignette index.

b03d9c5

Update .travis.yml

1e245fd

grabear changed the title ~~WIP Joss branch~~ Joss branch Feb 21, 2019

grabear mentioned this pull request Feb 21, 2019

select_if(<logical vector>) tidyverse/dplyr#4213

Closed

Updated node labeling for heat trees

18dd2d6

sdhutchins mentioned this pull request Feb 22, 2019

Update dev-master to master. #83

Merged

grabear added 2 commits February 22, 2019 17:44

Merge branch 'joss-branch' of https://github.com/vallenderlab/Microbi…

a627c35

…omeR into joss-branch

Updated DESCRIPTION and travis build.

997e668

grabear closed this Feb 26, 2019

This was referenced Feb 26, 2019

Dependency Issues. #84

Closed

JOSS submission and dplyr fix. #85

Merged

sdhutchins deleted the joss-branch branch March 1, 2019 00:10

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Joss branch#79

Joss branch#79
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grabear commented Feb 19, 2019

Uh oh!

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grabear commented Feb 19, 2019

MicrobiomeR 0.5.0

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sdhutchins commented Feb 20, 2019

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