library(immunarch)
#> Loading required package: ggplot2
#> Loading required package: dplyr
#>
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#>
#> filter, lag
#> The following objects are masked from 'package:base':
#>
#> intersect, setdiff, setequal, union
#> Loading required package: dtplyr
#> Loading required package: data.table
#>
#> Attaching package: 'data.table'
#> The following objects are masked from 'package:dplyr':
#>
#> between, first, last
#> Loading required package: patchwork
data(immdata)
align <- immdata$data %>% seqCluster(seqDist(immdata$data),
.perc_similarity = 0.6) %>% repGermline(.threads = 8) %>%
repAlignLineage(.min_lineage_sequences = 2, .align_threads = 8)
#> Warning: There was 1 warning in `mutate()`.
#> ℹ In argument: `length_value = map_chr(.y, ~ifelse(all(.x == .x[1]), yes =
#> .x[1], no = glue("range_{min(.x)}:{max(.x)}")))`.
#> Caused by warning:
#> ! Automatic coercion from integer to character was deprecated in purrr 1.0.0.
#> ℹ Please use an explicit call to `as.character()` within `map_chr()` instead.
#> ℹ The deprecated feature was likely used in the immunarch package.
#> Please report the issue at <https://github.com/immunomind/immunarch/issues>.
#> Error in `map2()`:
#> ℹ In index: 1.
#> ℹ With name: A2-i129.
#> Caused by error in `get()`:
#> ! object 'generate_germline_sequence' not found
Created on 2024-04-17 with reprex v2.1.0
Session info
``` r sessioninfo::session_info() #> ─ Session info ─────────────────────────────────────────────────────────────── #> setting value #> version R version 4.3.2 (2023-10-31) #> os Ubuntu 22.04.3 LTS #> system x86_64, linux-gnu #> ui X11 #> language (EN) #> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz Etc/UTC #> date 2024-04-17 #> pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date (UTC) lib source #> abind 1.4-5 2016-07-21 [1] RSPM (R 4.3.0) #> ape 5.7-1 2023-03-13 [1] RSPM (R 4.3.0) #> backports 1.4.1 2021-12-13 [1] RSPM (R 4.3.0) #> broom 1.0.5 2023-06-09 [1] RSPM (R 4.3.0) #> car 3.1-2 2023-03-30 [1] RSPM (R 4.3.0) #> carData 3.0-5 2022-01-06 [1] RSPM (R 4.3.0) #> cellranger 1.1.0 2016-07-27 [1] RSPM (R 4.3.0) #> circlize 0.4.16 2024-02-20 [1] RSPM (R 4.3.0) #> class 7.3-22 2023-05-03 [2] CRAN (R 4.3.2) #> cli 3.6.2 2023-12-11 [1] RSPM (R 4.3.0) #> cluster 2.1.4 2022-08-22 [2] CRAN (R 4.3.2) #> codetools 0.2-19 2023-02-01 [2] CRAN (R 4.3.2) #> colorspace 2.1-0 2023-01-23 [1] RSPM (R 4.3.0) #> data.table * 1.15.0 2024-01-30 [1] RSPM (R 4.3.0) #> DEoptimR 1.1-3 2023-10-07 [1] RSPM (R 4.3.0) #> digest 0.6.34 2024-01-11 [1] RSPM (R 4.3.0) #> diptest 0.77-0 2023-11-27 [1] RSPM (R 4.3.0) #> doParallel 1.0.17 2022-02-07 [1] RSPM (R 4.3.0) #> dplyr * 1.1.4 2023-11-17 [1] RSPM (R 4.3.0) #> dtplyr * 1.3.1 2023-03-22 [1] RSPM (R 4.3.0) #> ellipsis 0.3.2 2021-04-29 [1] RSPM (R 4.3.0) #> evaluate 0.23 2023-11-01 [1] RSPM (R 4.3.0) #> factoextra 1.0.7 2020-04-01 [1] RSPM (R 4.3.0) #> fansi 1.0.6 2023-12-08 [1] RSPM (R 4.3.0) #> farver 2.1.1 2022-07-06 [1] RSPM (R 4.3.0) #> fastmap 1.1.1 2023-02-24 [1] RSPM (R 4.3.0) #> fastmatch 1.1-4 2023-08-18 [1] RSPM (R 4.3.0) #> flexmix 2.3-19 2023-03-16 [1] RSPM (R 4.3.0) #> foreach 1.5.2 2022-02-02 [1] RSPM (R 4.3.0) #> fpc 2.2-11 2023-12-15 [1] RSPM (R 4.3.0) #> fs 1.6.3 2023-07-20 [1] RSPM (R 4.3.0) #> generics 0.1.3 2022-07-05 [1] RSPM (R 4.3.0) #> ggalluvial 0.12.5 2023-02-22 [1] RSPM (R 4.3.0) #> ggforce 0.4.1 2022-10-04 [1] RSPM (R 4.3.0) #> ggplot2 * 3.4.4 2023-10-12 [1] RSPM (R 4.3.0) #> ggpubr 0.6.0 2023-02-10 [1] RSPM (R 4.3.0) #> ggraph 2.1.0 2022-10-09 [1] RSPM (R 4.3.0) #> ggrepel 0.9.5 2024-01-10 [1] RSPM (R 4.3.0) #> ggseqlogo 0.2 2024-02-09 [1] RSPM (R 4.3.0) #> ggsignif 0.6.4 2022-10-13 [1] RSPM (R 4.3.0) #> GlobalOptions 0.1.2 2020-06-10 [1] RSPM (R 4.3.0) #> glue 1.7.0 2024-01-09 [1] RSPM (R 4.3.0) #> graphlayouts 1.1.0 2024-01-19 [1] RSPM (R 4.3.0) #> gridExtra 2.3 2017-09-09 [1] RSPM (R 4.3.0) #> gtable 0.3.4 2023-08-21 [1] RSPM (R 4.3.0) #> hms 1.1.3 2023-03-21 [1] RSPM (R 4.3.0) #> htmltools 0.5.7 2023-11-03 [1] RSPM (R 4.3.0) #> httpuv 1.6.14 2024-01-26 [1] RSPM (R 4.3.0) #> igraph 2.0.1.1 2024-01-30 [1] RSPM (R 4.3.0) #> immunarch * 0.9.1 2024-03-18 [1] RSPM (R 4.3.0) #> iterators 1.0.14 2022-02-05 [1] RSPM (R 4.3.0) #> jsonlite 1.8.8 2023-12-04 [1] RSPM (R 4.3.0) #> kernlab 0.9-32 2023-01-31 [1] RSPM (R 4.3.0) #> knitr 1.45 2023-10-30 [1] RSPM (R 4.3.0) #> later 1.3.2 2023-12-06 [1] RSPM (R 4.3.0) #> lattice 0.21-9 2023-10-01 [2] CRAN (R 4.3.2) #> lifecycle 1.0.4 2023-11-07 [1] RSPM (R 4.3.0) #> magrittr 2.0.3 2022-03-30 [1] RSPM (R 4.3.0) #> MASS 7.3-60 2023-05-04 [2] CRAN (R 4.3.2) #> Matrix 1.6-4 2023-11-30 [1] RSPM (R 4.3.0) #> mclust 6.1 2024-02-23 [1] RSPM (R 4.3.0) #> mime 0.12 2021-09-28 [1] RSPM (R 4.3.0) #> modeltools 0.2-23 2020-03-05 [1] RSPM (R 4.3.0) #> munsell 0.5.0 2018-06-12 [1] RSPM (R 4.3.0) #> nlme 3.1-163 2023-08-09 [2] CRAN (R 4.3.2) #> nnet 7.3-19 2023-05-03 [2] CRAN (R 4.3.2) #> patchwork * 1.2.0 2024-01-08 [1] RSPM (R 4.3.0) #> phangorn 2.11.1 2023-01-23 [1] RSPM (R 4.3.0) #> pheatmap 1.0.12 2019-01-04 [1] RSPM (R 4.3.0) #> pillar 1.9.0 2023-03-22 [1] RSPM (R 4.3.0) #> pkgconfig 2.0.3 2019-09-22 [1] RSPM (R 4.3.0) #> plyr 1.8.9 2023-10-02 [1] RSPM (R 4.3.0) #> polyclip 1.10-6 2023-09-27 [1] RSPM (R 4.3.0) #> prabclus 2.3-3 2023-10-24 [1] RSPM (R 4.3.0) #> promises 1.2.1 2023-08-10 [1] RSPM (R 4.3.0) #> purrr 1.0.2 2023-08-10 [1] RSPM (R 4.3.0) #> quadprog 1.5-8 2019-11-20 [1] RSPM (R 4.3.0) #> R.cache 0.16.0 2022-07-21 [1] RSPM #> R.methodsS3 1.8.2 2022-06-13 [1] RSPM #> R.oo 1.26.0 2024-01-24 [1] RSPM (R 4.3.0) #> R.utils 2.12.3 2023-11-18 [1] RSPM #> R6 2.5.1 2021-08-19 [1] RSPM (R 4.3.0) #> RColorBrewer 1.1-3 2022-04-03 [1] RSPM (R 4.3.0) #> Rcpp 1.0.12 2024-01-09 [1] RSPM (R 4.3.0) #> readr 2.1.5 2024-01-10 [1] RSPM (R 4.3.0) #> readxl 1.4.3 2023-07-06 [1] RSPM (R 4.3.0) #> reprex 2.1.0 2024-01-11 [1] RSPM (R 4.3.0) #> reshape2 1.4.4 2020-04-09 [1] RSPM (R 4.3.0) #> rlang 1.1.3 2024-01-10 [1] RSPM (R 4.3.0) #> rlist 0.4.6.2 2021-09-03 [1] RSPM (R 4.3.0) #> rmarkdown 2.25 2023-09-18 [1] RSPM #> robustbase 0.99-2 2024-01-27 [1] RSPM (R 4.3.0) #> rstatix 0.7.2 2023-02-01 [1] RSPM (R 4.3.0) #> scales 1.3.0 2023-11-28 [1] RSPM (R 4.3.0) #> sessioninfo 1.2.2 2021-12-06 [1] RSPM (R 4.3.0) #> shape 1.4.6 2021-05-19 [1] RSPM (R 4.3.0) #> shiny 1.8.0 2023-11-17 [1] RSPM (R 4.3.0) #> shinythemes 1.2.0 2021-01-25 [1] RSPM (R 4.3.0) #> stringdist 0.9.12 2023-11-28 [1] RSPM (R 4.3.0) #> stringi 1.8.3 2023-12-11 [1] RSPM (R 4.3.0) #> stringr 1.5.1 2023-11-14 [1] RSPM (R 4.3.0) #> styler 1.10.2 2023-08-29 [1] RSPM #> tibble 3.2.1 2023-03-20 [1] RSPM (R 4.3.0) #> tidygraph 1.3.1 2024-01-30 [1] RSPM (R 4.3.0) #> tidyr 1.3.1 2024-01-24 [1] RSPM (R 4.3.0) #> tidyselect 1.2.0 2022-10-10 [1] RSPM (R 4.3.0) #> tweenr 2.0.2 2022-09-06 [1] RSPM (R 4.3.0) #> tzdb 0.4.0 2023-05-12 [1] RSPM (R 4.3.0) #> UpSetR 1.4.0 2019-05-22 [1] RSPM (R 4.3.0) #> utf8 1.2.4 2023-10-22 [1] RSPM (R 4.3.0) #> uuid 1.2-0 2024-01-14 [1] RSPM (R 4.3.0) #> vctrs 0.6.5 2023-12-01 [1] RSPM (R 4.3.0) #> viridis 0.6.5 2024-01-29 [1] RSPM (R 4.3.0) #> viridisLite 0.4.2 2023-05-02 [1] RSPM (R 4.3.0) #> withr 3.0.0 2024-01-16 [1] RSPM (R 4.3.0) #> xfun 0.41 2023-11-01 [1] RSPM (R 4.3.0) #> xtable 1.8-4 2019-04-21 [1] RSPM (R 4.3.0) #> yaml 2.3.8 2023-12-11 [1] RSPM (R 4.3.0) #> #> [1] /usr/local/lib/R/site-library #> [2] /usr/local/lib/R/library #> #> ────────────────────────────────────────────────────────────────────────────── ```