Error when running overviewPerIndividualQC function

[dietmarfdz]

Describe the bug
While following your pdf (19/06/2019) when I run all the commands in the document for the demo data you provide, I get the following error:

overview_individuals <- overviewPerIndividualQC(fail_individuals, interactive=TRUE)

Error in start_col:end_col : argument of length 0
Además: Warning message:
In valid.data(rep(units, length.out = length(x)), data) :
  time limit arrived    #translated into english

The first plots (those generated with fail_individuals) are OK but the coordinates for both axis (x & y) shown for the right plot shown in "Relatedness estimated as pairwise IBD (PI_HAT) are not exactly the same than the ones shown in your tutorial.

Also, when running

overview_marker <- overviewPerMarkerQC(fail_markers, interactive=TRUE)

No error is given but no plot is shown.

overview_marker

$nr_fail_samples
[1] 2343

$fail_QC
           SNP_missingness hwe maf
rs4074137                1   0   0
rs7540009                1   0   1
rs12077700               1   0   1
rs10399878               1   0   1
...
...

I am using plink_1.9_20190617.

Am I doing something wrong?

sessionInfo()

R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=es_ES.UTF-8       LC_NUMERIC=C               LC_TIME=es_ES.UTF-8        LC_COLLATE=es_ES.UTF-8     LC_MONETARY=es_ES.UTF-8   
 [6] LC_MESSAGES=es_ES.UTF-8    LC_PAPER=es_ES.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] plinkQC_0.2.2

loaded via a namespace (and not attached):
[1] Rcpp_1.0.1        pillar_1.4.2      compiler_3.6.1    plyr_1.8.4        R.methodsS3_1.7.1 R.utils_2.9.0     tools_3.6.1       sys_3.3          
[9] digest_0.6.19     tibble_2.1.3      gtable_0.3.0      pkgconfig_2.0.2   rlang_0.4.0       ggrepel_0.8.1     yaml_2.2.0        xfun_0.7         
[17] gridExtra_2.3     UpSetR_1.4.0      dplyr_0.8.3       knitr_1.23        grid_3.6.1        getopt_1.20.3     cowplot_1.0.0     tidyselect_0.2.5 
[25] glue_1.3.1        optparse_1.6.4    data.table_1.12.2 R6_2.4.0          polyclip_1.10-0   ggplot2_3.2.1     purrr_0.3.2       tweenr_1.0.1     
[33] farver_1.1.0      magrittr_1.5      scales_1.0.0      MASS_7.3-51.4     assertthat_0.2.1  ggforce_0.3.1     colorspace_1.4-1  labeling_0.3     
[41] lazyeval_0.2.2    munsell_0.5.0     crayon_1.3.4      R.oo_1.22.0

[HannahVMeyer]

I will look into the differences in plots between vignettes and the sample data. I updated the data at some point and might have not recompiled the vignettes.

Could you try downloading the latest github version of plinkQC (0.2.3) via:

devttools::install_github("HannahVMeyer/plinkQC")

and see if the plotting works and the error remains?

Thank you

[dietmarfdz]

I followed your instructions in another computer and right now I get the following error:

overview_individuals <- overviewPerIndividualQC(fail_individuals, interactive=TRUE)
Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length

I do not know if this error is due to executing this in another computer or because of the different installation. I will check it tomorrow...

However, now when running:

overview_marker <- overviewPerMarkerQC(fail_markers, interactive=TRUE)
Warning message:
In drawGTree(x) : time limit arrived (#translated from my R version)

I obtain the plot.

sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=es_ES.UTF-8       LC_NUMERIC=C               LC_TIME=es_ES.UTF-8        LC_COLLATE=es_ES.UTF-8    
 [5] LC_MONETARY=es_ES.UTF-8    LC_MESSAGES=es_ES.UTF-8    LC_PAPER=es_ES.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] plinkQC_0.2.3

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.2        pillar_1.4.2      compiler_3.6.1    plyr_1.8.4        R.methodsS3_1.7.1 R.utils_2.9.0    
 [7] tools_3.6.1       sys_3.3           digest_0.6.21     tibble_2.1.3      gtable_0.3.0      pkgconfig_2.0.3  
[13] rlang_0.4.0       rstudioapi_0.10   ggrepel_0.8.1     gridExtra_2.3     UpSetR_1.4.0      dplyr_0.8.3      
[19] grid_3.6.1        getopt_1.20.3     cowplot_1.0.0     tidyselect_0.2.5  glue_1.3.1        optparse_1.6.4   
[25] data.table_1.12.2 R6_2.4.0          polyclip_1.10-0   ggplot2_3.2.1     purrr_0.3.2       tweenr_1.0.1     
[31] farver_1.1.0      magrittr_1.5      scales_1.0.0      MASS_7.3-51.4     assertthat_0.2.1  ggforce_0.3.1    
[37] colorspace_1.4-1  labeling_0.3      lazyeval_0.2.2    munsell_0.5.0     crayon_1.3.4      R.oo_1.22.0

[HannahVMeyer]

Thanks for following up on this and checking. I found the issue now (missing stringsAsFactors=FALSE). I added it on the dev branch, would you mind downloading the dev-version with

devtools::install_github("HannahVMeyer/plinkQC", ref="dev")

Thanks!

[dietmarfdz]

Now it works!!!
Thanks