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drieslab / Giotto

Spatial omics analysis toolbox
https://drieslab.github.io/Giotto_website/
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coord_fix_ratio does not work as expected #972

Open kaizen89 opened 1 week ago

kaizen89 commented 1 week ago

I tried multiple values for coord_fix_ratio but it does not change the aspect of the plot.

GiottoVisuals::spatFeatPlot2D(xenium_gobj,
               expression_values = 'raw',show_plot = T,
               feats = "CD3E", cow_n_col = 1, point_size = 1, coord_fix_ratio = 0.5)

However, using coord_fix_ratio inside GiottoVisuals::spatFeatPlot2D_single does behave as expected, so I suspect it is related to cowplot.

R version 4.1.1 (2021-08-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.6 LTS

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=fr_FR.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
[1] Giotto_4.0.8       GiottoClass_0.3.1  dplyr_1.1.4        Seurat_5.1.0       SeuratObject_5.0.2 sp_2.1-4           ggplot2_3.5.1      patchwork_1.2.0   

loaded via a namespace (and not attached):
  [1] backports_1.5.0        spam_2.10-0            circlize_0.4.16        systemfonts_1.1.0      plyr_1.8.9             igraph_2.0.3           lazyeval_0.2.2        
  [8] splines_4.1.1          RcppHNSW_0.6.0         RApiSerialize_0.1.3    listenv_0.9.1          scattermore_1.2        digest_0.6.35          htmltools_0.5.8.1     
 [15] magick_2.8.3           fansi_1.0.6            magrittr_2.0.3         checkmate_2.3.1        tensor_1.5             paletteer_1.6.0        cluster_2.1.2         
 [22] ROCR_1.0-11            globals_0.16.3         RcppParallel_5.1.7     matrixStats_1.3.0      R.utils_2.12.3         timechange_0.3.0       spatstat.sparse_3.0-3 
 [29] scCustomize_2.1.2      colorspace_2.1-0       rappdirs_0.3.3         ggrepel_0.9.5          textshaping_0.4.0      xfun_0.45              jsonlite_1.8.8        
 [36] progressr_0.14.0       spatstat.data_3.0-4    stringfish_0.16.0      survival_3.2-13        zoo_1.8-12             glue_1.7.0             polyclip_1.10-6       
 [43] gtable_0.3.5           GiottoVisuals_0.2.3    leiden_0.4.3.1         future.apply_1.11.2    shape_1.4.6.1          abind_1.4-5            scales_1.3.0          
 [50] colorRamp2_0.1.0       GiottoUtils_0.1.8      spatstat.random_3.2-3  miniUI_0.1.1.1         Rcpp_1.0.12            viridisLite_0.4.2      xtable_1.8-4          
 [57] reticulate_1.37.0      dotCall64_1.1-1        htmlwidgets_1.6.4      httr_1.4.7             RColorBrewer_1.1-3     ica_1.0-3              farver_2.1.2          
 [64] R.methodsS3_1.8.2      pkgconfig_2.0.3        uwot_0.2.2             deldir_2.0-4           utf8_1.2.4             janitor_2.2.0          labeling_0.4.3        
 [71] tidyselect_1.2.1       rlang_1.1.4            reshape2_1.4.4         later_1.3.2            munsell_0.5.1          tools_4.1.1            cli_3.6.2             
 [78] ggprism_1.0.5          dbscan_1.1-12          generics_0.1.3         ggridges_0.5.6         stringr_1.5.1          fastmap_1.2.0          ragg_1.3.2            
 [85] goftest_1.2-3          rematch2_2.1.2         knitr_1.47             fitdistrplus_1.1-11    purrr_1.0.2            RANN_2.6.1             pbapply_1.7-2         
 [92] future_1.33.2          nlme_3.1-152           mime_0.12              R.oo_1.26.0            ggrastr_1.0.2          compiler_4.1.1         rstudioapi_0.16.0     
 [99] beeswarm_0.4.0         plotly_4.10.4          png_0.1-8              spatstat.utils_3.0-5   tibble_3.2.1           stringi_1.8.4          RSpectra_0.16-1       
[106] forcats_1.0.0          lattice_0.20-44        Matrix_1.6-5           vctrs_0.6.5            pillar_1.9.0           lifecycle_1.0.4        spatstat.geom_3.2-9   
[113] lmtest_0.9-40          GlobalOptions_0.1.2    RcppAnnoy_0.0.22       data.table_1.15.4      cowplot_1.1.3          irlba_2.3.5.1          httpuv_1.6.15         
[120] R6_2.5.1               qs_0.26.3              promises_1.3.0         renv_0.13.2            KernSmooth_2.23-20     gridExtra_2.3          vipor_0.4.7           
[127] parallelly_1.37.1      codetools_0.2-18       fastDummies_1.7.3      MASS_7.3-54            gtools_3.9.5           withr_3.0.0            presto_1.0.0          
[134] sctransform_0.4.1      parallel_4.1.1         terra_1.7-78           grid_4.1.1             tidyr_1.3.1            snakecase_0.11.1       Rtsne_0.17            
[141] spatstat.explore_3.2-7 shiny_1.8.1.1          lubridate_1.9.3        ggbeeswarm_0.7.2