Error in purrr::map()

[dollykc]

Hi Dr. Gosselin, I downloaded sticklebacks_Danish.vcf from https://datadryad.org/stash/dataset/doi:10.5061%2Fdryad.kp11q and the strata.stickleback.tsv from https://www.dropbox.com/s/ely3wp4j4tulkrc/strata.stickleback.tsv?dl=0. I executed the following code

library("grur") ibm <- grur::missing_visualization( data = "sticklebacks_Danish.vcf", strata = "strata.stickleback.tsv", parallel.core = 1L)

And I get the following error Analysing percentage missing ... Error in purrr::map(): i In index: 1. Caused by error in env_get(): ! object 'term' not found Run rlang::last_error() to see where the error occurred. Warning message: package ‘fstcore’ was built under R version 4.1.3

rlang::last_error() Backtrace:

1. grur::missing_visualization(...)
   16. tidyr:::pivot_wider.data.frame(...)
   17. tidyr::build_wider_spec(...)
   18. tidyselect::eval_select(enquo(names_from), data)
   19. tidyselect:::eval_select_impl(...)
   20. tidyselect:::vars_select_eval(...)
   21. tidyselect:::walk_data_tree(expr, data_mask, context_mask)
   22. tidyselect:::eval_sym(expr, data_mask, context_mask)
   23. rlang::env_get(env, name, default = missing_arg(), inherit = TRUE)

I tried again with a dataset of mine from Stacks population output and a popmap turned into a strata file and I got the same result.

The entire output I got is below

################################################################################ ######################## grur::missing_visualization ########################### ################################################################################ Execution date/time: 20230106@1055

::grurmissing_visualization function call arguments: data = sticklebacks_Danish.vcf strata = strata.stickleback.tsv strata.select = POP_ID distance.method = euclidean ind.missing.geno.threshold = 2, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90 filename = NULL parallel.core = 1 write.plot = TRUE

Default "..." arguments assigned in ::grurmissing_visualization: path.folder = NULL

Folder created: missing_visualization_20230106@1055 File written: grur_missing_visualization_data_args_20230106@1055.tsv

Importing data Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML' Also defined by ‘S4Vectors’ Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML' Also defined by ‘S4Vectors’ Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML' Also defined by ‘S4Vectors’ Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML' Also defined by ‘S4Vectors’ Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML' Also defined by ‘S4Vectors’ Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML' Also defined by ‘S4Vectors’

Reading VCF...

Data summary: number of samples: 177 number of markers: 31802

Filter monomorphic markers Number of individuals / strata / chrom / locus / SNP: Blacklisted: 0 / 0 / 0 / 0 / 0

Filter common markers: Number of individuals / strata / chrom / locus / SNP: Blacklisted: 0 / 0 / 0 / 0 / 0

Number of chromosome/contig/scaffold: 196 Number of locus: 17095 Number of markers: 31802 Number of strata: 8 Number of individuals: 177

Number of ind/strata: HAD = 21 HAL = 19 KIB = 17 KRO = 20 MOS = 20 MAR = 20 NOR = 20 ODD = 40

Number of duplicate id: 0 radiator Genomic Data Structure (GDS) file: radiator_20230106@1055.gds File written: individuals qc info and stats summary
File written: individuals qc plot

Informations: Number of populations: 8 Number of individuals: 177 Number of ind/pop: HAD = 21 HAL = 19 KIB = 17 KRO = 20 MOS = 20 MAR = 20 NOR = 20 ODD = 40

Number of duplicate id: 0 Number of chrom/scaffolds: 196 Number of locus: 17095 Number of SNPs: 31802

Proportion of missing genotypes (overall): 0.022169

Identity-by-missingness (IBM) analysis using Principal Coordinate Analysis (PCoA)... fstcore package v0.9.12 (OpenMP detected, using 12 threads) Generating Identity by missingness plot Redundancy analysis... Redundancy Analysis using strata: POP_ID RDA model formula: data.pcoa$vectors ~ POP_ID Permutation test for Redundancy Analysis using strata: POP_ID

Hypothesis based on the strata provided Null Hypothesis (H0): No pattern of missingness in the data between strata Alternative Hypothesis (H1): Presence of pattern(s) of missingness in the data between strata

A tibble: 1 x 3

STRATA VARIANCE P_VALUE

1 POP_ID 0.00597 0.000999 note: low p-value -> reject the null hypothesis Analysing percentage missing ... Error in `purrr::map()`: i In index: 1. Caused by error in `env_get()`: ! object 'term' not found Run `rlang::last_error()` to see where the error occurred. Warning message: package ‘fstcore’ was built under R version 4.1.3 Computation time, overall: 46 sec ############################ missing_visualization #############################

[clorenzo1]

Hi, I am getting the exact same error when trying to do the same thing with a vcf produced from STACKS2 and a popmap also turned into a strata file. Any updates on this?

Cheers

[thierrygosselin]

I'll have a look at it over the weekend thanks for reporting