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plot_poppr_msn(): add error for unfiltered data with filtered msn #140

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zkamvar opened this issue Jun 22, 2017 · 0 comments
Open

plot_poppr_msn(): add error for unfiltered data with filtered msn #140

zkamvar opened this issue Jun 22, 2017 · 0 comments
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@zkamvar
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lots of refactoring 😅 nitpick 🤔 🤔 🤔

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@zkamvar
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zkamvar commented Jun 22, 2017

There needs to be a sensible error for the use of unfiltered data and a filtered msn when using plot_poppr_msn()

Currently, it gives unhelpful warnings:

library("poppr")
#> Loading required package: adegenet
#> Loading required package: ade4
#> 
#>    /// adegenet 2.1.0 is loaded ////////////
#> 
#>    > overview: '?adegenet'
#>    > tutorials/doc/questions: 'adegenetWeb()' 
#>    > bug reports/feature requests: adegenetIssues()
#> This is poppr version 2.4.1.99.2. To get started, type package?poppr
#> OMP parallel support: available
#> 
#> This version of poppr is under development.
#> If you find any bugs, please report them at https://github.com/grunwaldlab/poppr/issues
data("partial_clone")
pcd <- diss.dist(partial_clone)
pcmsn <- poppr.msn(partial_clone, threshold = 5, distmat = pcd, showplot = FALSE)
plot_poppr_msn(partial_clone, pcmsn)
#> Warning in vertex.size + 6 * 8 * log10(nchar(labels) + 1): longer object
#> length is not a multiple of shorter object length
#> Warning in layout[, 1] + label.dist * cos(-label.degree) * (vertex.size + :
#> longer object length is not a multiple of shorter object length
#> Warning in vertex.size + 6 * 8 * log10(nchar(labels) + 1): longer object
#> length is not a multiple of shorter object length
#> Warning in layout[, 2] + label.dist * sin(-label.degree) * (vertex.size + :
#> longer object length is not a multiple of shorter object length

Session info 
devtools::session_info()
#> Session info -------------------------------------------------------------
#>  setting  value                       
#>  version  R version 3.4.0 (2017-04-21)
#>  system   x86_64, darwin15.6.0        
#>  ui       X11                         
#>  language (EN)                        
#>  collate  en_US.UTF-8                 
#>  tz       America/Chicago             
#>  date     2017-06-21
#> Packages -----------------------------------------------------------------
#>  package    * version    date      
#>  ade4       * 1.7-6      2017-03-23
#>  adegenet   * 2.1.0      2017-05-06
#>  ape          4.1        2017-02-14
#>  assertthat   0.2.0      2017-04-11
#>  backports    1.1.0      2017-05-22
#>  base       * 3.4.0      2017-04-21
#>  bitops       1.0-6      2013-08-17
#>  boot         1.3-19     2017-04-21
#>  cluster      2.0.6      2017-03-16
#>  coda         0.19-1     2016-12-08
#>  colorspace   1.3-2      2016-12-14
#>  compiler     3.4.0      2017-04-21
#>  datasets   * 3.4.0      2017-04-21
#>  DBI          0.6-1      2017-04-01
#>  deldir       0.1-14     2017-04-22
#>  devtools     1.13.2     2017-06-02
#>  digest       0.6.12     2017-01-27
#>  dplyr        0.7.0      2017-06-09
#>  evaluate     0.10       2016-10-11
#>  expm         0.999-2    2017-03-29
#>  fastmatch    1.1-0      2017-01-28
#>  formatR      1.5        2017-04-25
#>  gdata        2.18.0     2017-06-06
#>  ggplot2      2.2.1.9000 2017-06-19
#>  glue         1.0.0      2017-04-17
#>  gmodels      2.16.2     2015-07-22
#>  graphics   * 3.4.0      2017-04-21
#>  grDevices  * 3.4.0      2017-04-21
#>  grid         3.4.0      2017-04-21
#>  gtable       0.2.0      2016-02-26
#>  gtools       3.5.0      2015-05-29
#>  htmltools    0.3.6      2017-04-28
#>  httpuv       1.3.3      2015-08-04
#>  igraph       1.0.1      2015-06-26
#>  knitr        1.16       2017-05-18
#>  lattice      0.20-35    2017-03-25
#>  lazyeval     0.2.0      2016-06-12
#>  LearnBayes   2.15       2014-05-29
#>  magrittr     1.5        2014-11-22
#>  MASS         7.3-47     2017-04-21
#>  Matrix       1.2-10     2017-04-28
#>  memoise      1.1.0      2017-04-21
#>  methods    * 3.4.0      2017-04-21
#>  mgcv         1.8-17     2017-02-08
#>  mime         0.5        2016-07-07
#>  munsell      0.4.3      2016-02-13
#>  nlme         3.1-131    2017-02-06
#>  parallel     3.4.0      2017-04-21
#>  pegas        0.10       2017-05-03
#>  permute      0.9-4      2016-09-09
#>  phangorn     2.2.0      2017-04-03
#>  plyr         1.8.4      2016-06-08
#>  poppr      * 2.4.1.99-2 2017-05-06
#>  quadprog     1.5-5      2013-04-17
#>  R6           2.2.2      2017-06-17
#>  Rcpp         0.12.11    2017-05-22
#>  RCurl        1.95-4.8   2016-03-01
#>  reshape2     1.4.2      2016-10-22
#>  rlang        0.1.1      2017-05-18
#>  rmarkdown    1.6        2017-06-15
#>  rprojroot    1.2        2017-01-16
#>  scales       0.4.1      2016-11-09
#>  seqinr       3.3-6      2017-04-06
#>  shiny        1.0.3      2017-04-26
#>  sp           1.2-4      2016-12-22
#>  spdep        0.6-13     2017-04-25
#>  splines      3.4.0      2017-04-21
#>  stats      * 3.4.0      2017-04-21
#>  stringi      1.1.5      2017-04-07
#>  stringr      1.2.0      2017-02-18
#>  tibble       1.3.3      2017-05-28
#>  tools        3.4.0      2017-04-21
#>  utils      * 3.4.0      2017-04-21
#>  vegan        2.4-3      2017-04-07
#>  withr        1.0.2      2016-06-20
#>  XML          3.98-1.7   2017-05-03
#>  xtable       1.8-2      2016-02-05
#>  yaml         2.1.14     2016-11-12
#>  source                                  
#>  CRAN (R 3.4.0)                          
#>  Github (thibautjombart/adegenet@e07c139)
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  local                                   
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  local                                   
#>  local                                   
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  Github (tidyverse/ggplot2@d1b847b)      
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  local                                   
#>  local                                   
#>  local                                   
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  local                                   
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  local                                   
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  Github (grunwaldlab/poppr@cd4cba2)      
#>  CRAN (R 3.4.0)                          
#>  cran (@2.2.2)                           
#>  cran (@0.12.11)                         
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  cran (@1.6)                             
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  local                                   
#>  local                                   
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  local                                   
#>  local                                   
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)                          
#>  CRAN (R 3.4.0)
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@zkamvar zkamvar

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lots of refactoring 😅 nitpick 🤔 🤔 🤔
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