ggrepel
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Published
20 hours ago •
slowkow
slowkow
ggrepel does not put labels at correct position of dotplot
Summary
When creating a plot with geom_dotplot, geom_text_repel does not draw the label arrows to the exact point location but rather to the center. (See points B1,B2,B3) Is there any way to do this?
Minimal code example
Here is the minimum amount of code needed to demonstrate the issue:
df=data.frame(name=c("A1","A2","B1","B2","B3"),value=c(1,2,2,2,2),group=c("A","A","B","B","B"))
ggplot(df,aes(x=group,y=value,label=name))+
geom_dotplot(binaxis='y', stackdir='center', dotsize=0.7)+
geom_text_repel(aes(segment.color="red"),box.padding = 1,max.overlaps=10)
Here is an image of the output produced by the code:
Suggestions
I tried extracting the correct positions from geom_dotplot to feed them to geom_text_repel which did not work, so now I am out of ideas.
Version information
Here is the output from sessionInfo() in my R session:
sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Linux Mint 19
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=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=de_DE.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] grid tcltk parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggpubr_0.4.0 waffle_1.0.1 scales_1.1.1
[4] ggsci_2.9 PCAtools_2.2.0 ggrepel_0.9.1
[7] flextable_0.6.6 RColorBrewer_1.1-2 VennDiagram_1.6.20
[10] futile.logger_1.4.3 Mfuzz_2.50.0 DynDoc_1.68.0
[13] widgetTools_1.68.0 e1071_1.7-6 pheatmap_1.0.12
[16] ggplot2_3.3.3 Rmisc_1.5 plyr_1.8.6
[19] lattice_0.20-44 tidyr_1.1.3 biomaRt_2.47.9
[22] DESeq2_1.30.1 SummarizedExperiment_1.20.0 Biobase_2.50.0
[25] MatrixGenerics_1.2.1 matrixStats_0.58.0 GenomicRanges_1.42.0
[28] GenomeInfoDb_1.26.7 IRanges_2.24.1 S4Vectors_0.28.1
[31] BiocGenerics_0.36.1 tximport_1.18.0 data.table_1.14.0
loaded via a namespace (and not attached):
[1] readxl_1.3.1 uuid_0.1-4 backports_1.2.1 BiocFileCache_1.14.0
[5] systemfonts_1.0.2 splines_4.0.3 BiocParallel_1.24.1 digest_0.6.27
[9] htmltools_0.5.1.1 fansi_0.4.2 magrittr_2.0.1 memoise_2.0.0
[13] openxlsx_4.2.3 limma_3.46.0 annotate_1.68.0 extrafont_0.17
[17] officer_0.3.18 extrafontdb_1.0 prettyunits_1.1.1 colorspace_2.0-1
[21] blob_1.2.1 rappdirs_0.3.3 haven_2.4.1 xfun_0.23
[25] dplyr_1.0.6 crayon_1.4.1 RCurl_1.98-1.3 genefilter_1.72.1
[29] survival_3.2-11 glue_1.4.2 gtable_0.3.0 zlibbioc_1.36.0
[33] XVector_0.30.0 DelayedArray_0.16.3 car_3.0-10 BiocSingular_1.6.0
[37] Rttf2pt1_1.3.8 abind_1.4-5 futile.options_1.0.1 DBI_1.1.1
[41] rstatix_0.7.0 Rcpp_1.0.6 xtable_1.8-4 progress_1.2.2
[45] dqrng_0.3.0 foreign_0.8-81 bit_4.0.4 rsvd_1.0.5
[49] proxy_0.4-25 DT_0.18.1 htmlwidgets_1.5.3 httr_1.4.2
[53] ellipsis_0.3.2 pkgconfig_2.0.3 XML_3.99-0.6 farver_2.1.0
[57] dbplyr_2.1.1 locfit_1.5-9.4 utf8_1.2.1 tidyselect_1.1.1
[61] labeling_0.4.2 rlang_0.4.11 tkWidgets_1.68.0 reshape2_1.4.4
[65] AnnotationDbi_1.52.0 cellranger_1.1.0 munsell_0.5.0 tools_4.0.3
[69] cachem_1.0.5 cli_2.5.0 generics_0.1.0 RSQLite_2.2.7
[73] broom_0.7.6 evaluate_0.14 stringr_1.4.0 fastmap_1.1.0
[77] knitr_1.33 bit64_4.0.5 zip_2.1.1 purrr_0.3.4
[81] sparseMatrixStats_1.2.1 formatR_1.9 xml2_1.3.2 compiler_4.0.3
[85] rstudioapi_0.13 curl_4.3.1 ggsignif_0.6.1 tibble_3.1.2
[89] geneplotter_1.68.0 stringi_1.6.2 forcats_0.5.1 gdtools_0.2.3
[93] Matrix_1.3-3 vctrs_0.3.8 pillar_1.6.1 lifecycle_1.0.0
[97] cowplot_1.1.1 bitops_1.0-7 irlba_2.3.3 R6_2.5.0
[101] rio_0.5.26 gridExtra_2.3 lambda.r_1.2.4 assertthat_0.2.1
[105] withr_2.4.2 GenomeInfoDbData_1.2.4 hms_1.1.0 beachmat_2.6.4
[109] class_7.3-19 rmarkdown_2.8 DelayedMatrixStats_1.12.3 carData_3.0-4
[113] base64enc_0.1-3
@svenbioinf Have you considered whether any other visual presentation might be a better way to communicates your message to your audience? Sometimes tables are more effective than graphical figures.
This issue won't be fixed, because as far as I know, there is no ggplot2::position_*() function that is complementary to ggplot2::geom_dotplot().
Typically, the strategy in this situation is to first define a position and then draw a plot, e.g.:
my_pos <- ggplot2::position_dodge(width = 0.5)
ggplot(...) + geom_point(position = my_pos) + geom_text_repel(position = my_pos)
My reprex below is a hacky attempt to get something along these lines to work, but I don't recommend it.
Please consider reviewing related posts:
-
A duplicate ggrepel issue https://github.com/slowkow/ggrepel/issues/139
-
Related posts from Stack Overflow:
- https://stackoverflow.com/questions/44991607/how-do-i-label-the-dots-of-a-geom-dotplot-in-ggplot2
- https://stackoverflow.com/questions/48545286/geom-dotplot-with-text-instead-of-dots
library(ggrepel)
#> Loading required package: ggplot2
df <- data.frame(
name = c("A1", "A2", "B1", "B2", "B3"),
value = c(1, 2, 2, 2, 2),
group = c("A", "A", "B", "B", "B")
)
ggplot(df, aes(x = group, y = value, label = name)) +
geom_dotplot(binaxis = "y", stackdir = "center", dotsize = 0.7) +
geom_text_repel(aes(segment.color = "red"), box.padding = 1, max.overlaps = 10)
#> Bin width defaults to 1/30 of the range of the data. Pick better value with `binwidth`.
ggplot(df, aes(x = group, y = value, label = name)) +
geom_dotplot(binaxis = "y", stackdir = "center", dotsize = 0.7) +
geom_text_repel(
aes(segment.color = "red", group = name),
box.padding = 1, max.overlaps = 10,
position = position_dodge(width = 0.1)
)
#> Bin width defaults to 1/30 of the range of the data. Pick better value with `binwidth`.
Created on 2021-09-30 by the reprex package (v0.3.0)
Session info
devtools::session_info()
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#> setting value
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#> os macOS Catalina 10.15.7
#> system x86_64, darwin17.0
#> ui X11
#> language (EN)
#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz America/New_York
#> date 2021-09-30
#>
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#> assertthat 0.2.1 2019-03-21 [2] CRAN (R 4.0.2)
#> blob 1.2.1 2020-01-20 [2] CRAN (R 4.0.2)
#> callr 3.5.1 2020-10-13 [2] CRAN (R 4.0.2)
#> cli 2.3.1 2021-02-23 [1] CRAN (R 4.0.3)
#> colorspace 2.0-0 2020-11-11 [2] CRAN (R 4.0.2)
#> crayon 1.4.1 2021-02-08 [1] CRAN (R 4.0.2)
#> curl 4.3 2019-12-02 [2] CRAN (R 4.0.1)
#> DBI 1.1.0 2019-12-15 [2] CRAN (R 4.0.2)
#> debugme 1.1.0 2017-10-22 [1] CRAN (R 4.0.2)
#> desc 1.2.0 2018-05-01 [2] CRAN (R 4.0.2)
#> devtools 2.3.0 2020-04-10 [2] CRAN (R 4.0.2)
#> digest 0.6.27 2020-10-24 [2] CRAN (R 4.0.2)
#> dplyr 1.0.4 2021-02-02 [1] CRAN (R 4.0.2)
#> ellipsis 0.3.1 2020-05-15 [2] CRAN (R 4.0.2)
#> evaluate 0.14 2019-05-28 [2] CRAN (R 4.0.1)
#> fansi 0.4.2 2021-01-15 [1] CRAN (R 4.0.2)
#> farver 2.0.3 2020-01-16 [2] CRAN (R 4.0.2)
#> fs 1.5.0 2020-07-31 [1] CRAN (R 4.0.2)
#> generics 0.1.0 2020-10-31 [2] CRAN (R 4.0.2)
#> ggplot2 * 3.3.5 2021-06-25 [1] CRAN (R 4.0.2)
#> ggrepel * 0.9.1.9999 2021-01-22 [1] local
#> glue 1.4.2 2020-08-27 [2] CRAN (R 4.0.2)
#> gtable 0.3.0 2019-03-25 [2] CRAN (R 4.0.2)
#> highr 0.8 2019-03-20 [2] CRAN (R 4.0.2)
#> htmltools 0.5.1.1 2021-01-22 [1] CRAN (R 4.0.2)
#> httr 1.4.2 2020-07-20 [2] CRAN (R 4.0.2)
#> knitr 1.31 2021-01-27 [1] CRAN (R 4.0.2)
#> labeling 0.4.2 2020-10-20 [2] CRAN (R 4.0.2)
#> lifecycle 1.0.0 2021-02-15 [1] CRAN (R 4.0.2)
#> magrittr 2.0.1.9000 2020-12-15 [1] Github (tidyverse/magrittr@bb1c86a)
#> memoise 1.1.0.9000 2020-12-15 [1] Github (r-lib/memoise@0901e3f)
#> mime 0.10 2021-02-13 [1] CRAN (R 4.0.2)
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#> pillar 1.5.0 2021-02-22 [1] CRAN (R 4.0.3)
#> pkgbuild 1.1.0 2020-07-13 [2] CRAN (R 4.0.2)
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#> sessioninfo 1.1.1 2018-11-05 [2] CRAN (R 4.0.2)
#> stringi 1.5.3 2020-09-09 [2] CRAN (R 4.0.2)
#> stringr 1.4.0 2019-02-10 [2] CRAN (R 4.0.2)
#> testthat 3.0.0 2020-10-31 [2] CRAN (R 4.0.2)
#> tibble 3.0.6 2021-01-29 [1] CRAN (R 4.0.2)
#> tidyselect 1.1.0 2020-05-11 [2] CRAN (R 4.0.2)
#> usethis 1.6.1 2020-04-29 [2] CRAN (R 4.0.2)
#> utf8 1.1.4 2018-05-24 [2] CRAN (R 4.0.2)
#> vctrs 0.3.6 2020-12-17 [1] CRAN (R 4.0.2)
#> withr 2.4.1 2021-01-26 [1] CRAN (R 4.0.2)
#> xfun 0.21 2021-02-10 [1] CRAN (R 4.0.2)
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#>
#> [1] /Users/kamil/Library/R/4.0/library
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