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Add raster.dpias parameter for VlnPlot #9656

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lucygarner opened this issue Jan 29, 2025 · 2 comments
Open

Add raster.dpias parameter for VlnPlot #9656

lucygarner opened this issue Jan 29, 2025 · 2 comments
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enhancement New feature or request

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@lucygarner
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Hi,

It would be great if raster.dpi could be added as a parameter for VlnPlot. The size of the rasterized points is not modified by the pt.size argument.

Best wishes,
Lucy
@lucygarner lucygarner added the enhancement New feature or request label Jan 29, 2025
@samuel-marsh
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Hi Lucy,

This is definitely good enhancement to have but it doesn't have an effect on the point size displayed only the dpi for the rastered output layer/image See first reprex below. I have created PR to add parameter to VlnPlot because this is still good parameter to have when saving rastered images.

In my testing pt.size still works for changing the size of rastered points. See second reprex below.

Best,
Sam

Changing raster.dpi

library(tidyverse)
#> Warning: package 'lubridate' was built under R version 4.4.1
library(Seurat)
#> Loading required package: SeuratObject
#> Loading required package: sp
#> 'SeuratObject' was built with package 'Matrix' 1.7.0 but the current
#> version is 1.7.1; it is recomended that you reinstall 'SeuratObject' as
#> the ABI for 'Matrix' may have changed
#> 
#> Attaching package: 'SeuratObject'
#> The following objects are masked from 'package:base':
#> 
#>     intersect, t


pbmc <- pbmc3k.SeuratData::pbmc3k.final
pbmc <- UpdateSeuratObject(pbmc)
#> Validating object structure
#> Updating object slots
#> Ensuring keys are in the proper structure
#> Updating matrix keys for DimReduc 'pca'
#> Updating matrix keys for DimReduc 'umap'
#> Warning: Assay RNA changing from Assay to Assay
#> Warning: Graph RNA_nn changing from Graph to Graph
#> Warning: Graph RNA_snn changing from Graph to Graph
#> Warning: DimReduc pca changing from DimReduc to DimReduc
#> Warning: DimReduc umap changing from DimReduc to DimReduc
#> Ensuring keys are in the proper structure
#> Ensuring feature names don't have underscores or pipes
#> Updating slots in RNA
#> Updating slots in RNA_nn
#> Setting default assay of RNA_nn to RNA
#> Updating slots in RNA_snn
#> Setting default assay of RNA_snn to RNA
#> Updating slots in pca
#> Updating slots in umap
#> Setting umap DimReduc to global
#> Setting assay used for NormalizeData.RNA to RNA
#> Setting assay used for FindVariableFeatures.RNA to RNA
#> Setting assay used for ScaleData.RNA to RNA
#> Setting assay used for RunPCA.RNA to RNA
#> Setting assay used for JackStraw.RNA.pca to RNA
#> No assay information could be found for ScoreJackStraw
#> Warning: Adding a command log without an assay associated with it
#> Setting assay used for FindNeighbors.RNA.pca to RNA
#> No assay information could be found for FindClusters
#> Warning: Adding a command log without an assay associated with it
#> Setting assay used for RunUMAP.RNA.pca to RNA
#> Validating object structure for Assay 'RNA'
#> Validating object structure for Graph 'RNA_nn'
#> Validating object structure for Graph 'RNA_snn'
#> Validating object structure for DimReduc 'pca'
#> Validating object structure for DimReduc 'umap'
#> Object representation is consistent with the most current Seurat version


VlnPlot(pbmc, features = "ACTB", raster = T, raster.dpi = 5)

VlnPlot(pbmc, features = "ACTB", raster = T, raster.dpi = 300)

Created on 2025-02-04 with reprex v2.1.1

Session info 
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.4.0 (2024-04-24)
#>  os       macOS Monterey 12.7.6
#>  system   x86_64, darwin20
#>  ui       X11
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       America/New_York
#>  date     2025-02-04
#>  pandoc   3.2 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/x86_64/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package           * version date (UTC) lib source
#>  abind               1.4-8   2024-09-12 [1] CRAN (R 4.4.1)
#>  beeswarm            0.4.0   2021-06-01 [1] CRAN (R 4.4.0)
#>  Cairo               1.6-2   2023-11-28 [1] CRAN (R 4.4.0)
#>  cli                 3.6.3   2024-06-21 [1] CRAN (R 4.4.0)
#>  cluster             2.1.8   2024-12-11 [1] CRAN (R 4.4.1)
#>  codetools           0.2-20  2024-03-31 [1] CRAN (R 4.4.0)
#>  colorspace          2.1-1   2024-07-26 [1] CRAN (R 4.4.0)
#>  cowplot             1.1.3   2024-01-22 [1] CRAN (R 4.4.0)
#>  curl                6.1.0   2025-01-06 [1] CRAN (R 4.4.1)
#>  data.table          1.16.4  2024-12-06 [1] CRAN (R 4.4.1)
#>  deldir              2.0-4   2024-02-28 [1] CRAN (R 4.4.0)
#>  digest              0.6.37  2024-08-19 [1] CRAN (R 4.4.1)
#>  dotCall64           1.2     2024-10-04 [1] CRAN (R 4.4.1)
#>  dplyr             * 1.1.4   2023-11-17 [1] CRAN (R 4.4.0)
#>  evaluate            1.0.3   2025-01-10 [1] CRAN (R 4.4.1)
#>  farver              2.1.2   2024-05-13 [1] CRAN (R 4.4.0)
#>  fastDummies         1.7.5   2025-01-20 [1] CRAN (R 4.4.1)
#>  fastmap             1.2.0   2024-05-15 [1] CRAN (R 4.4.0)
#>  fitdistrplus        1.2-2   2025-01-07 [1] CRAN (R 4.4.1)
#>  forcats           * 1.0.0   2023-01-29 [1] CRAN (R 4.4.0)
#>  fs                  1.6.5   2024-10-30 [1] CRAN (R 4.4.1)
#>  future              1.34.0  2024-07-29 [1] CRAN (R 4.4.0)
#>  future.apply        1.11.3  2024-10-27 [1] CRAN (R 4.4.1)
#>  generics            0.1.3   2022-07-05 [1] CRAN (R 4.4.0)
#>  ggbeeswarm          0.7.2   2023-04-29 [1] CRAN (R 4.4.0)
#>  ggplot2           * 3.5.1   2024-04-23 [1] CRAN (R 4.4.0)
#>  ggrastr             1.0.2   2023-06-01 [1] CRAN (R 4.4.0)
#>  ggrepel             0.9.6   2024-09-07 [1] CRAN (R 4.4.1)
#>  ggridges            0.5.6   2024-01-23 [1] CRAN (R 4.4.0)
#>  globals             0.16.3  2024-03-08 [1] CRAN (R 4.4.0)
#>  glue                1.8.0   2024-09-30 [1] CRAN (R 4.4.1)
#>  goftest             1.2-3   2021-10-07 [1] CRAN (R 4.4.0)
#>  gridExtra           2.3     2017-09-09 [1] CRAN (R 4.4.0)
#>  gtable              0.3.6   2024-10-25 [1] CRAN (R 4.4.1)
#>  hms                 1.1.3   2023-03-21 [1] CRAN (R 4.4.0)
#>  htmltools           0.5.8.1 2024-04-04 [1] CRAN (R 4.4.0)
#>  htmlwidgets         1.6.4   2023-12-06 [1] CRAN (R 4.4.0)
#>  httpuv              1.6.15  2024-03-26 [1] CRAN (R 4.4.0)
#>  httr                1.4.7   2023-08-15 [1] CRAN (R 4.4.0)
#>  ica                 1.0-3   2022-07-08 [1] CRAN (R 4.4.0)
#>  igraph              2.1.2   2024-12-07 [1] CRAN (R 4.4.1)
#>  irlba               2.3.5.1 2022-10-03 [1] CRAN (R 4.4.0)
#>  jsonlite            1.8.9   2024-09-20 [1] CRAN (R 4.4.1)
#>  KernSmooth          2.23-26 2025-01-01 [1] CRAN (R 4.4.1)
#>  knitr               1.49    2024-11-08 [1] CRAN (R 4.4.1)
#>  labeling            0.4.3   2023-08-29 [1] CRAN (R 4.4.0)
#>  later               1.4.1   2024-11-27 [1] CRAN (R 4.4.1)
#>  lattice             0.22-6  2024-03-20 [1] CRAN (R 4.4.0)
#>  lazyeval            0.2.2   2019-03-15 [1] CRAN (R 4.4.0)
#>  lifecycle           1.0.4   2023-11-07 [1] CRAN (R 4.4.0)
#>  listenv             0.9.1   2024-01-29 [1] CRAN (R 4.4.0)
#>  lmtest              0.9-40  2022-03-21 [1] CRAN (R 4.4.0)
#>  lubridate         * 1.9.4   2024-12-08 [1] CRAN (R 4.4.1)
#>  magrittr            2.0.3   2022-03-30 [1] CRAN (R 4.4.0)
#>  MASS                7.3-64  2025-01-04 [1] CRAN (R 4.4.1)
#>  Matrix              1.7-1   2024-10-18 [1] CRAN (R 4.4.1)
#>  matrixStats         1.5.0   2025-01-07 [1] CRAN (R 4.4.1)
#>  mime                0.12    2021-09-28 [1] CRAN (R 4.4.0)
#>  miniUI              0.1.1.1 2018-05-18 [1] CRAN (R 4.4.0)
#>  munsell             0.5.1   2024-04-01 [1] CRAN (R 4.4.0)
#>  nlme                3.1-166 2024-08-14 [1] CRAN (R 4.4.1)
#>  parallelly          1.41.0  2024-12-18 [1] CRAN (R 4.4.1)
#>  patchwork           1.3.0   2024-09-16 [1] CRAN (R 4.4.1)
#>  pbapply             1.7-2   2023-06-27 [1] CRAN (R 4.4.0)
#>  pbmc3k.SeuratData   3.1.4   2024-05-01 [1] local
#>  pillar              1.10.1  2025-01-07 [1] CRAN (R 4.4.1)
#>  pkgconfig           2.0.3   2019-09-22 [1] CRAN (R 4.4.0)
#>  plotly              4.10.4  2024-01-13 [1] CRAN (R 4.4.0)
#>  plyr                1.8.9   2023-10-02 [1] CRAN (R 4.4.0)
#>  png                 0.1-8   2022-11-29 [1] CRAN (R 4.4.0)
#>  polyclip            1.10-7  2024-07-23 [1] CRAN (R 4.4.0)
#>  progressr           0.15.1  2024-11-22 [1] CRAN (R 4.4.1)
#>  promises            1.3.2   2024-11-28 [1] CRAN (R 4.4.1)
#>  purrr             * 1.0.2   2023-08-10 [1] CRAN (R 4.4.0)
#>  R6                  2.5.1   2021-08-19 [1] CRAN (R 4.4.0)
#>  RANN                2.6.2   2024-08-25 [1] CRAN (R 4.4.1)
#>  RColorBrewer        1.1-3   2022-04-03 [1] CRAN (R 4.4.0)
#>  Rcpp                1.0.14  2025-01-12 [1] CRAN (R 4.4.1)
#>  RcppAnnoy           0.0.22  2024-01-23 [1] CRAN (R 4.4.0)
#>  RcppHNSW            0.6.0   2024-02-04 [1] CRAN (R 4.4.0)
#>  readr             * 2.1.5   2024-01-10 [1] CRAN (R 4.4.0)
#>  reprex              2.1.1   2024-07-06 [1] CRAN (R 4.4.0)
#>  reshape2            1.4.4   2020-04-09 [1] CRAN (R 4.4.0)
#>  reticulate          1.40.0  2024-11-15 [1] CRAN (R 4.4.1)
#>  rlang               1.1.5   2025-01-17 [1] CRAN (R 4.4.1)
#>  rmarkdown           2.29    2024-11-04 [1] CRAN (R 4.4.1)
#>  ROCR                1.0-11  2020-05-02 [1] CRAN (R 4.4.0)
#>  RSpectra            0.16-2  2024-07-18 [1] CRAN (R 4.4.0)
#>  rstudioapi          0.17.1  2024-10-22 [1] CRAN (R 4.4.1)
#>  Rtsne               0.17    2023-12-07 [1] CRAN (R 4.4.0)
#>  scales              1.3.0   2023-11-28 [1] CRAN (R 4.4.0)
#>  scattermore         1.2     2023-06-12 [1] CRAN (R 4.4.0)
#>  sctransform         0.4.1   2023-10-19 [1] CRAN (R 4.4.0)
#>  sessioninfo         1.2.2   2021-12-06 [1] CRAN (R 4.4.0)
#>  Seurat            * 5.2.1   2025-02-04 [1] Github (samuel-marsh/seurat@4d3e935)
#>  SeuratObject      * 5.0.2   2024-05-08 [1] CRAN (R 4.4.0)
#>  shiny               1.10.0  2024-12-14 [1] CRAN (R 4.4.1)
#>  sp                * 2.1-4   2024-04-30 [1] CRAN (R 4.4.0)
#>  spam                2.11-1  2025-01-20 [1] CRAN (R 4.4.1)
#>  spatstat.data       3.1-4   2024-11-15 [1] CRAN (R 4.4.1)
#>  spatstat.explore    3.3-4   2025-01-08 [1] CRAN (R 4.4.1)
#>  spatstat.geom       3.3-5   2025-01-18 [1] CRAN (R 4.4.1)
#>  spatstat.random     3.3-2   2024-09-18 [1] CRAN (R 4.4.1)
#>  spatstat.sparse     3.1-0   2024-06-21 [1] CRAN (R 4.4.0)
#>  spatstat.univar     3.1-1   2024-11-05 [1] CRAN (R 4.4.1)
#>  spatstat.utils      3.1-2   2025-01-08 [1] CRAN (R 4.4.1)
#>  stringi             1.8.4   2024-05-06 [1] CRAN (R 4.4.0)
#>  stringr           * 1.5.1   2023-11-14 [1] CRAN (R 4.4.0)
#>  survival            3.8-3   2024-12-17 [1] CRAN (R 4.4.1)
#>  tensor              1.5     2012-05-05 [1] CRAN (R 4.4.0)
#>  tibble            * 3.2.1   2023-03-20 [1] CRAN (R 4.4.0)
#>  tidyr             * 1.3.1   2024-01-24 [1] CRAN (R 4.4.0)
#>  tidyselect          1.2.1   2024-03-11 [1] CRAN (R 4.4.0)
#>  tidyverse         * 2.0.0   2023-02-22 [1] CRAN (R 4.4.0)
#>  timechange          0.3.0   2024-01-18 [1] CRAN (R 4.4.0)
#>  tzdb                0.4.0   2023-05-12 [1] CRAN (R 4.4.0)
#>  uwot                0.2.2   2024-04-21 [1] CRAN (R 4.4.0)
#>  vctrs               0.6.5   2023-12-01 [1] CRAN (R 4.4.0)
#>  vipor               0.4.7   2023-12-18 [1] CRAN (R 4.4.0)
#>  viridisLite         0.4.2   2023-05-02 [1] CRAN (R 4.4.0)
#>  withr               3.0.2   2024-10-28 [1] CRAN (R 4.4.1)
#>  xfun                0.50.5  2025-01-15 [1] https://yihui.r-universe.dev (R 4.4.2)
#>  xml2                1.3.6   2023-12-04 [1] CRAN (R 4.4.0)
#>  xtable              1.8-4   2019-04-21 [1] CRAN (R 4.4.0)
#>  yaml                2.3.10  2024-07-26 [1] CRAN (R 4.4.0)
#>  zoo                 1.8-12  2023-04-13 [1] CRAN (R 4.4.0)
#> 
#>  [1] /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────

Changing pt.size with raster = TRUE

library(tidyverse)
#> Warning: package 'lubridate' was built under R version 4.4.1
library(Seurat)
#> Loading required package: SeuratObject
#> Loading required package: sp
#> 'SeuratObject' was built with package 'Matrix' 1.7.0 but the current
#> version is 1.7.1; it is recomended that you reinstall 'SeuratObject' as
#> the ABI for 'Matrix' may have changed
#> 
#> Attaching package: 'SeuratObject'
#> The following objects are masked from 'package:base':
#> 
#>     intersect, t


pbmc <- pbmc3k.SeuratData::pbmc3k.final
pbmc <- UpdateSeuratObject(pbmc)
#> Validating object structure
#> Updating object slots
#> Ensuring keys are in the proper structure
#> Updating matrix keys for DimReduc 'pca'
#> Updating matrix keys for DimReduc 'umap'
#> Warning: Assay RNA changing from Assay to Assay
#> Warning: Graph RNA_nn changing from Graph to Graph
#> Warning: Graph RNA_snn changing from Graph to Graph
#> Warning: DimReduc pca changing from DimReduc to DimReduc
#> Warning: DimReduc umap changing from DimReduc to DimReduc
#> Ensuring keys are in the proper structure
#> Ensuring feature names don't have underscores or pipes
#> Updating slots in RNA
#> Updating slots in RNA_nn
#> Setting default assay of RNA_nn to RNA
#> Updating slots in RNA_snn
#> Setting default assay of RNA_snn to RNA
#> Updating slots in pca
#> Updating slots in umap
#> Setting umap DimReduc to global
#> Setting assay used for NormalizeData.RNA to RNA
#> Setting assay used for FindVariableFeatures.RNA to RNA
#> Setting assay used for ScaleData.RNA to RNA
#> Setting assay used for RunPCA.RNA to RNA
#> Setting assay used for JackStraw.RNA.pca to RNA
#> No assay information could be found for ScoreJackStraw
#> Warning: Adding a command log without an assay associated with it
#> Setting assay used for FindNeighbors.RNA.pca to RNA
#> No assay information could be found for FindClusters
#> Warning: Adding a command log without an assay associated with it
#> Setting assay used for RunUMAP.RNA.pca to RNA
#> Validating object structure for Assay 'RNA'
#> Validating object structure for Graph 'RNA_nn'
#> Validating object structure for Graph 'RNA_snn'
#> Validating object structure for DimReduc 'pca'
#> Validating object structure for DimReduc 'umap'
#> Object representation is consistent with the most current Seurat version


VlnPlot(pbmc, features = "ACTB", raster = T, pt.size = 1)

VlnPlot(pbmc, features = "ACTB", raster = T, pt.size = 5)

Created on 2025-02-04 with reprex v2.1.1

Session info 
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.4.0 (2024-04-24)
#>  os       macOS Monterey 12.7.6
#>  system   x86_64, darwin20
#>  ui       X11
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       America/New_York
#>  date     2025-02-04
#>  pandoc   3.2 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/x86_64/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package           * version date (UTC) lib source
#>  abind               1.4-8   2024-09-12 [1] CRAN (R 4.4.1)
#>  beeswarm            0.4.0   2021-06-01 [1] CRAN (R 4.4.0)
#>  Cairo               1.6-2   2023-11-28 [1] CRAN (R 4.4.0)
#>  cli                 3.6.3   2024-06-21 [1] CRAN (R 4.4.0)
#>  cluster             2.1.8   2024-12-11 [1] CRAN (R 4.4.1)
#>  codetools           0.2-20  2024-03-31 [1] CRAN (R 4.4.0)
#>  colorspace          2.1-1   2024-07-26 [1] CRAN (R 4.4.0)
#>  cowplot             1.1.3   2024-01-22 [1] CRAN (R 4.4.0)
#>  curl                6.1.0   2025-01-06 [1] CRAN (R 4.4.1)
#>  data.table          1.16.4  2024-12-06 [1] CRAN (R 4.4.1)
#>  deldir              2.0-4   2024-02-28 [1] CRAN (R 4.4.0)
#>  digest              0.6.37  2024-08-19 [1] CRAN (R 4.4.1)
#>  dotCall64           1.2     2024-10-04 [1] CRAN (R 4.4.1)
#>  dplyr             * 1.1.4   2023-11-17 [1] CRAN (R 4.4.0)
#>  evaluate            1.0.3   2025-01-10 [1] CRAN (R 4.4.1)
#>  farver              2.1.2   2024-05-13 [1] CRAN (R 4.4.0)
#>  fastDummies         1.7.5   2025-01-20 [1] CRAN (R 4.4.1)
#>  fastmap             1.2.0   2024-05-15 [1] CRAN (R 4.4.0)
#>  fitdistrplus        1.2-2   2025-01-07 [1] CRAN (R 4.4.1)
#>  forcats           * 1.0.0   2023-01-29 [1] CRAN (R 4.4.0)
#>  fs                  1.6.5   2024-10-30 [1] CRAN (R 4.4.1)
#>  future              1.34.0  2024-07-29 [1] CRAN (R 4.4.0)
#>  future.apply        1.11.3  2024-10-27 [1] CRAN (R 4.4.1)
#>  generics            0.1.3   2022-07-05 [1] CRAN (R 4.4.0)
#>  ggbeeswarm          0.7.2   2023-04-29 [1] CRAN (R 4.4.0)
#>  ggplot2           * 3.5.1   2024-04-23 [1] CRAN (R 4.4.0)
#>  ggrastr             1.0.2   2023-06-01 [1] CRAN (R 4.4.0)
#>  ggrepel             0.9.6   2024-09-07 [1] CRAN (R 4.4.1)
#>  ggridges            0.5.6   2024-01-23 [1] CRAN (R 4.4.0)
#>  globals             0.16.3  2024-03-08 [1] CRAN (R 4.4.0)
#>  glue                1.8.0   2024-09-30 [1] CRAN (R 4.4.1)
#>  goftest             1.2-3   2021-10-07 [1] CRAN (R 4.4.0)
#>  gridExtra           2.3     2017-09-09 [1] CRAN (R 4.4.0)
#>  gtable              0.3.6   2024-10-25 [1] CRAN (R 4.4.1)
#>  hms                 1.1.3   2023-03-21 [1] CRAN (R 4.4.0)
#>  htmltools           0.5.8.1 2024-04-04 [1] CRAN (R 4.4.0)
#>  htmlwidgets         1.6.4   2023-12-06 [1] CRAN (R 4.4.0)
#>  httpuv              1.6.15  2024-03-26 [1] CRAN (R 4.4.0)
#>  httr                1.4.7   2023-08-15 [1] CRAN (R 4.4.0)
#>  ica                 1.0-3   2022-07-08 [1] CRAN (R 4.4.0)
#>  igraph              2.1.2   2024-12-07 [1] CRAN (R 4.4.1)
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#> ──────────────────────────────────────────────────────────────────────────────

@samuel-marsh samuel-marsh mentioned this issue Feb 4, 2025
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@samuel-marsh
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See PR #9665.

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