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Label's position is off in VolcanoPlot #268

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goepp opened this issue Jan 22, 2025 · 0 comments
Open

Label's position is off in VolcanoPlot #268

goepp opened this issue Jan 22, 2025 · 0 comments

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@goepp
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goepp commented Jan 22, 2025

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        
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