Label's position is off in VolcanoPlot #268
Description
First, thank you for developping SCP!
Bug description
The text annotation of the most differentially expressed genes on the VolcanoPlots is sometimes off.
Example from the help of VolcanoPlot:
data("pancreas_sub")
pancreas_sub <- RunDEtest(pancreas_sub, group_by = "CellType", only.pos = FALSE)
VolcanoPlot(pancreas_sub, group_by = "CellType")
On the first facet, the text label of "Map1b" and "Aplp1" is off.
Version of SCP
Tested on SCP 0.5.6.
sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: aarch64-apple-darwin20
Running under: macOS 15.2
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Europe/Berlin
tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] knitr_1.49 data.table_1.16.4 RColorBrewer_1.1-3 DESeq2_1.44.0 png_0.1-8 pheatmap_1.0.12
[7] SingleCellExperiment_1.26.0 SummarizedExperiment_1.34.0 Biobase_2.64.0 GenomicRanges_1.56.2 GenomeInfoDb_1.40.1 IRanges_2.38.1
[13] MatrixGenerics_1.16.0 matrixStats_1.5.0 S4Vectors_0.42.1 BiocGenerics_0.50.0 reshape2_1.4.4 edgeR_4.2.2
[19] limma_3.60.6 Matrix.utils_0.9.7 Matrix_1.7-1 cowplot_1.1.3 patchwork_1.3.0 lubridate_1.9.4
[25] forcats_1.0.0 dplyr_1.1.4 purrr_1.0.2 readr_2.1.5 tidyr_1.3.1 tibble_3.2.1
[31] tidyverse_2.0.0 BiocParallel_1.38.0 stringr_1.5.1 Seurat_5.2.0 SeuratObject_5.0.2 sp_2.1-4
[37] ggplot2_3.5.1 SCP_0.5.6
loaded via a namespace (and not attached):
[1] fs_1.6.5 spatstat.sparse_3.1-0 bitops_1.0-9 enrichplot_1.24.4 httr_1.4.7 doParallel_1.0.17 tools_4.4.1
[8] sctransform_0.4.1 R6_2.5.1 HDF5Array_1.32.1 lazyeval_0.2.2 uwot_0.2.2 rhdf5filters_1.16.0 GetoptLong_1.0.5
[15] withr_3.0.2 prettyunits_1.2.0 gridExtra_2.3 progressr_0.15.1 textshaping_0.4.1 cli_3.6.3 spatstat.explore_3.3-4
[22] fastDummies_1.7.4 scatterpie_0.2.4 labeling_0.4.3 spatstat.data_3.1-4 ggridges_0.5.6 pbapply_1.7-2 slingshot_2.12.0
[29] systemfonts_1.2.0 Rsamtools_2.20.0 yulab.utils_0.1.9 gson_0.1.0 DOSE_3.30.5 R.utils_2.12.3 parallelly_1.41.0
[36] rstudioapi_0.17.1 RSQLite_2.3.9 generics_0.1.3 gridGraphics_0.5-1 shape_1.4.6.1 ica_1.0-3 spatstat.random_3.3-2
[43] GO.db_3.19.1 abind_1.4-8 R.methodsS3_1.8.2 lifecycle_1.0.4 rhdf5_2.48.0 qvalue_2.36.0 SparseArray_1.4.8
[50] BiocFileCache_2.12.0 Rtsne_0.17 grid_4.4.1 blob_1.2.4 promises_1.3.2 crayon_1.5.3 miniUI_0.1.1.1
[57] lattice_0.22-6 KEGGREST_1.44.1 pillar_1.10.1 ComplexHeatmap_2.20.0 fgsea_1.30.0 rjson_0.2.23 future.apply_1.11.3
[64] codetools_0.2-20 fastmatch_1.1-6 glue_1.8.0 ggfun_0.1.8 spatstat.univar_3.1-1 vctrs_0.6.5 treeio_1.28.0
[71] spam_2.11-0 gtable_0.3.6 cachem_1.1.0 xfun_0.50 princurve_2.1.6 Signac_1.14.0 S4Arrays_1.4.1
[78] mime_0.12 tidygraph_1.3.1 survival_3.8-3 RcppRoll_0.3.1 iterators_1.0.14 statmod_1.5.0 fitdistrplus_1.2-2
[85] ROCR_1.0-11 nlme_3.1-166 ggtree_3.12.0 bit64_4.6.0-1 progress_1.2.3 filelock_1.0.3 RcppAnnoy_0.0.22
[92] R.cache_0.16.0 irlba_2.3.5.1 KernSmooth_2.23-26 colorspace_2.1-1 DBI_1.2.3 tidyselect_1.2.1 proxyC_0.4.1
[99] bit_4.5.0.1 compiler_4.4.1 curl_6.1.0 httr2_1.0.7 xml2_1.3.6 DelayedArray_0.30.1 plotly_4.10.4
[106] shadowtext_0.1.4 scales_1.3.0 lmtest_0.9-40 rappdirs_0.3.3 digest_0.6.37 goftest_1.2-3 spatstat.utils_3.1-2
[113] XVector_0.44.0 htmltools_0.5.8.1 pkgconfig_2.0.3 dbplyr_2.5.0 fastmap_1.2.0 rlang_1.1.4 GlobalOptions_0.1.2
[120] htmlwidgets_1.6.4 UCSC.utils_1.0.0 shiny_1.10.0 farver_2.1.2 zoo_1.8-12 jsonlite_1.8.9 GOSemSim_2.30.2
[127] R.oo_1.27.0 magrittr_2.0.3 GenomeInfoDbData_1.2.12 ggplotify_0.1.2 dotCall64_1.2 Rhdf5lib_1.26.0 munsell_0.5.1
[134] Rcpp_1.0.14 TrajectoryUtils_1.12.0 ape_5.8-1 ggnewscale_0.5.0 viridis_0.6.5 reticulate_1.40.0 stringi_1.8.4
[141] ggraph_2.2.1 zlibbioc_1.50.0 MASS_7.3-64 plyr_1.8.9 parallel_4.4.1 listenv_0.9.1 ggrepel_0.9.6
[148] deldir_2.0-4 Biostrings_2.72.1 graphlayouts_1.2.1 splines_4.4.1 tensor_1.5 hms_1.1.3 circlize_0.4.16
[155] locfit_1.5-9.10 igraph_2.1.2 spatstat.geom_3.3-4 RcppHNSW_0.6.0 biomaRt_2.60.1 evaluate_1.0.3 tzdb_0.4.0
[162] foreach_1.5.2 tweenr_2.0.3 httpuv_1.6.15 grr_0.9.5 RANN_2.6.2 polyclip_1.10-7 future_1.34.0
[169] clue_0.3-66 scattermore_1.2 ggforce_0.4.2 xtable_1.8-4 RSpectra_0.16-2 tidytree_0.4.6 later_1.4.1
[176] ragg_1.3.3 viridisLite_0.4.2 clusterProfiler_4.12.6 aplot_0.2.4 memoise_2.0.1 AnnotationDbi_1.66.0 cluster_2.1.8
[183] timechange_0.3.0 globals_0.16.3