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First, thank you for developping SCP!
The text annotation of the most differentially expressed genes on the VolcanoPlots is sometimes off.
VolcanoPlot
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.
Tested on SCP 0.5.6.
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
The text was updated successfully, but these errors were encountered:
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First, thank you for developping SCP!
Bug description
The text annotation of the most differentially expressed genes on the
VolcanoPlot
s is sometimes off.Example from the help of
VolcanoPlot
:On the first facet, the text label of "Map1b" and "Aplp1" is off.
Version of SCP
Tested on SCP 0.5.6.
sessionInfo()
The text was updated successfully, but these errors were encountered: