From 07c88912d2935cec7721d6355e6275b59bf15a30 Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Tue, 25 Jun 2024 08:04:53 +0000 Subject: [PATCH] cli-85346-130 --- 404.html | 6 +- articles/cytoviewer.html | 161 ++++++++++++++++++++------------------ articles/index.html | 6 +- authors.html | 8 +- index.html | 20 ++--- pkgdown.yml | 6 +- reference/cytoviewer.html | 10 +-- reference/index.html | 6 +- 8 files changed, 111 insertions(+), 112 deletions(-) diff --git a/404.html b/404.html index ed5d644..41386f8 100644 --- a/404.html +++ b/404.html @@ -6,7 +6,7 @@ Page not found (404) • cytoviewer - + @@ -32,7 +32,7 @@ cytoviewer - 1.3.3 + 1.5.0 @@ -88,7 +88,7 @@

Page not found (404)

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/articles/cytoviewer.html b/articles/cytoviewer.html index 2ebc3e8..7909a3a 100644 --- a/articles/cytoviewer.html +++ b/articles/cytoviewer.html @@ -6,7 +6,7 @@ cytoviewer - Interactive multi-channel image visualization in R • cytoviewer - + @@ -33,7 +33,7 @@ cytoviewer - 1.3.3 + 1.5.0 @@ -83,7 +83,7 @@

Nils Zurich
-

6 January 2024

+

25 June 2024

Source: vignettes/cytoviewer.Rmd @@ -114,17 +114,17 @@

Introductioncytomapper +

The cytoviewer package builds on top of the cytomapper Bioconductor package (Eling et al. 2020) and extends the static visualization strategies provided by cytomapper via an interactive Shiny application. The cytoviewer package leverages the image handling, analysis and visualization strategies provided by the -EBImage +EBImage Bioconductor package and offers interactive image visualization -strategies in a similar fashion as iSEE for -single-cell data. In addition, building up on SingleCellExperiment, -SpatialExperiment +strategies in a similar fashion as iSEE for +single-cell data. In addition, building up on SingleCellExperiment, +SpatialExperiment and cytomapper::CytoImageList classes, the cytoviewer package integrates into the Bioconductor framework for single-cell and image analysis.

@@ -192,8 +192,9 @@

Application overviewimage downloads (Figure 2B).

-
-

Figure 1: cytoviewer interface and +

+Figure 1: cytoviewer interface and functionality. (A) The supported functionality (right) of cytoviewer depends on the data inputs (left). To match information between the objects, cell (cell_id) and image (img_id) identifiers can be provided. SCE/SPE = SingleCellExperiment/SpatialExperiment. (B) The graphical user interface of cytoviewer is divided into a body, header, and sidebar. The body of cytoviewer includes the image viewer, which has three tabs: Composite (Image-level), Channels (Image-level), and Mask (Cell-level). Zooming is supported for Composite and Mask tabs. The package version, R session information, help page, and a drop-down menu for image downloads are located in the header. The sidebar menu has controls for sample selection, image visualization, mask visualization, and general settings. Scale bar: 150 µm (C) cytoviewer supports different viewing modes. Top: The “channels” tab of image-level visualization displays individual channels. Shown are Ecad (magenta), CD8a (cyan), and CD68 (yellow) marking tumor cells, CD8+ T cells, and myeloid cells, respectively. Center: The “composite” tab of image-level visualization visualizes image composites combining multiple channels. These composite images can be overlayed with cell outlines, which can be colored by cell-specific metadata. Shown here are cell outlines colored by cell area (continous value) and cell type (categorical value; tumor cells in white). Channel color settings are as follows for all markers: Contrast: 2,5; Brightness: 1; Gamma: 1.2. Bottom: The “mask” tab can be used to visualize segmentation masks that can be colored by cell-specific metadata. Shown here are segmentation masks colored by cell area (continuous) and cell type (categorical; tumor cells in magenta). Scale bars: 150 µm. (D) “Image appearance” controls can be used to add legends or titles and to change the scale bar length for image-level (top) and cell level (bottom) visualization. The cell-level mask plot depicts tumor (magenta), myeloid (yellow), and CD8+ T cells (cyan). Scale bars: 100 µm. Adapted from (Meyer, Eling, and Bodenmiller 2023)
+Figure 1: cytoviewer interface and functionality. (A) The supported functionality (right) of cytoviewer depends on the data inputs (left). To match information between the objects, cell (cell_id) and image (img_id) @@ -225,14 +226,15 @@

Application overview(Meyer, Eling, and Bodenmiller 2023)

+CD8+ T cells (cyan). Scale bars: 100 µm. Adapted from (Meyer, Eling, and Bodenmiller 2023) +

Data input format

-

The cytoviewer package combines objects of SingleCellExperiment, -SpatialExperiment -and cytomapper::CytoImageList classes (from cytomapper) +

The cytoviewer package combines objects of SingleCellExperiment, +SpatialExperiment +and cytomapper::CytoImageList classes (from cytomapper) to visualize image- and cell-level information.

The cytoviewer function takes up to five arguments.

@@ -267,9 +269,9 @@

Data input format

For more detailed information on the input objects, please refer to -the respective documentation (e.g. the vignettes of the cytomapper -or SingleCellExperiment/ -SpatialExperiment +the respective documentation (e.g. the vignettes of the cytomapper +or SingleCellExperiment/ +SpatialExperiment packages).

In the Read in data section, we provide example code to directly read in images and masks (e.g. in .tiff format) @@ -333,7 +335,7 @@

InstallationExample dataset

For visualization purposes, we will use a toy dataset provided by the -cytomapper +cytomapper package.

The dataset contains 3 images of \(100\mu{m}\) x \(100\mu{m}\) dimensions with 362 segmented cells and pixel-intensities for 5 proteins: H3, CD99, PIN, CD8a, and @@ -347,7 +349,7 @@

Example datasetpancreasSCE.

For more detailed information on the dataset, please refer to the respective documentation (e.g. via ?pancreasImages or the -vignette of the cytomapper +vignette of the cytomapper package).

We also provide example code to directly read in images and masks (e.g. in .tiff format) into a CytoImageList object and @@ -433,16 +435,18 @@

Image-level visualization -

Figure 2: Image-level visualization - Basic -controls. The graphical user interface of cytoviewer for +

+Figure 2: Image-level visualization - Basic controls. The graphical user interface of cytoviewer for image-level-composite with basic controls. For image-level visualization, Ecad (magenta), CD8a (cyan) and CD68 (yellow) marking tumor cells, CD8+ T cells and myeloid cells, respectively, are shown and channel color settings are as follows for all markers: Contrast: 2,5; Brightness: 1; Gamma: 1.2. Note that the Composite tab is zoomable. Scale bars: 150 µm. Adapted from (Meyer, Eling, and Bodenmiller 2023)
+Figure 2: Image-level visualization - +Basic controls. The graphical user interface of cytoviewer for image-level-composite with basic controls. For image-level visualization, Ecad (magenta), CD8a (cyan) and CD68 (yellow) marking tumor cells, CD8+ T cells and myeloid cells, respectively, are shown and channel color settings are as follows for all markers: Contrast: 2,5; Brightness: 1; Gamma: 1.2. Note that the Composite tab is zoomable. Scale bars: 150 µm. Adapted from (Meyer, Eling, -and Bodenmiller 2023)

+and Bodenmiller 2023) +

In the advanced controls part, the user can choose to overlay the displayed images with provided segmentation @@ -452,8 +456,9 @@

Image-level visualization -

Figure 3: Image-level visualization - +

+Figure 3: Image-level visualization - Advanced controls. The graphical user interface of cytoviewer for image-level-composite with advanced controls. For image-level visualization, Ecad (magenta), CD8a (cyan) and CD68 (yellow) marking tumor cells, CD8+ T cells and myeloid cells, respectively, are shown and channel color settings are as follows for all markers: Contrast: 2,5; Brightness: 1; Gamma: 1.2. Note that the Composite tab is zoomable. Scale bars: 150 µm. Adapted from (Meyer, Eling, and Bodenmiller 2023)
+Figure 3: Image-level visualization - Advanced controls. The graphical user interface of cytoviewer for image-level-composite with advanced controls. For image-level visualization, Ecad (magenta), CD8a (cyan) and CD68 (yellow) marking @@ -461,7 +466,8 @@

Image-level visualization(Meyer, Eling, -and Bodenmiller 2023)

+and Bodenmiller 2023) +

@@ -474,13 +480,15 @@

Cell-level visualizationPlease note again that for categorical and continuous metadata entries the user can choose between discrete colors and continuous color palettes (viridis, inferno, plasma), respectively.

-
-

Figure 4: Cell-level visualization - Basic -controls. The graphical user interface of cytoviewer for +

+Figure 4: Cell-level visualization - Basic controls. The graphical user interface of cytoviewer for cell-level-mask with basic controls. For cell-level visualization, tumor cells (magenta) are highlighted. Note that the Mask tab is zoomable. Adapted from (Meyer, Eling, and Bodenmiller 2023)
+Figure 4: Cell-level visualization - +Basic controls. The graphical user interface of cytoviewer for cell-level-mask with basic controls. For cell-level visualization, tumor cells (magenta) are highlighted. Note that the Mask tab is zoomable. Adapted from (Meyer, Eling, and Bodenmiller -2023)

+2023) +
@@ -615,9 +623,9 @@

Run cytoviewer }

For more detailed information on the input objects, please refer to -the respective documentation (the vignettes of the cytomapper -or SingleCellExperiment/ -SpatialExperiment +the respective documentation (the vignettes of the cytomapper +or SingleCellExperiment/ +SpatialExperiment packages).

@@ -625,13 +633,13 @@

Run cytoviewer

Session info

-
## R version 4.3.2 (2023-10-31)
-## Platform: x86_64-apple-darwin20 (64-bit)
-## Running under: macOS Monterey 12.7.2
+
## R version 4.4.1 (2024-06-14)
+## Platform: aarch64-apple-darwin20
+## Running under: macOS Sonoma 14.5
 ## 
 ## Matrix products: default
-## BLAS:   /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib 
-## LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0
+## BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.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
@@ -646,53 +654,52 @@ 
Session info## other attached packages:
 ##  [1] cytomapper_1.14.0           SingleCellExperiment_1.24.0
 ##  [3] SummarizedExperiment_1.32.0 Biobase_2.62.0             
-##  [5] GenomicRanges_1.54.1        GenomeInfoDb_1.38.5        
+##  [5] GenomicRanges_1.54.1        GenomeInfoDb_1.38.8        
 ##  [7] IRanges_2.36.0              S4Vectors_0.40.2           
 ##  [9] BiocGenerics_0.48.1         MatrixGenerics_1.14.0      
-## [11] matrixStats_1.2.0           EBImage_4.44.0             
-## [13] cytoviewer_1.3.3            BiocStyle_2.30.0           
+## [11] matrixStats_1.3.0           EBImage_4.44.0             
+## [13] cytoviewer_1.5.0            BiocStyle_2.30.0           
 ## 
 ## loaded via a namespace (and not attached):
-##   [1] bitops_1.0-7             gridExtra_2.3            rlang_1.1.2             
+##   [1] bitops_1.0-7             gridExtra_2.3            rlang_1.1.4             
 ##   [4] magrittr_2.0.3           svgPanZoom_0.3.4         shinydashboard_0.7.2    
-##   [7] compiler_4.3.2           png_0.1-8                systemfonts_1.0.5       
-##  [10] fftwtools_0.9-11         vctrs_0.6.5              stringr_1.5.1           
-##  [13] pkgconfig_2.0.3          SpatialExperiment_1.12.0 crayon_1.5.2            
-##  [16] fastmap_1.1.1            magick_2.8.2             XVector_0.42.0          
-##  [19] ellipsis_0.3.2           fontawesome_0.5.2        utf8_1.2.4              
-##  [22] promises_1.2.1           rmarkdown_2.25           ggbeeswarm_0.7.2        
-##  [25] ragg_1.2.7               purrr_1.0.2              xfun_0.41               
-##  [28] zlibbioc_1.48.0          cachem_1.0.8             jsonlite_1.8.8          
-##  [31] later_1.3.2              rhdf5filters_1.14.1      DelayedArray_0.28.0     
-##  [34] Rhdf5lib_1.24.1          BiocParallel_1.36.0      terra_1.7-65            
-##  [37] jpeg_0.1-10              tiff_0.1-12              parallel_4.3.2          
-##  [40] R6_2.5.1                 bslib_0.6.1              stringi_1.8.3           
-##  [43] RColorBrewer_1.1-3       jquerylib_0.1.4          Rcpp_1.0.11             
-##  [46] bookdown_0.37            knitr_1.45               nnls_1.5                
-##  [49] httpuv_1.6.13            Matrix_1.6-1.1           tidyselect_1.2.0        
-##  [52] viridis_0.6.4            abind_1.4-5              yaml_2.3.8              
-##  [55] codetools_0.2-19         miniUI_0.1.1.1           lattice_0.21-9          
-##  [58] tibble_3.2.1             shiny_1.8.0              evaluate_0.23           
-##  [61] archive_1.1.7            desc_1.4.3               shinycssloaders_1.0.0   
-##  [64] pillar_1.9.0             BiocManager_1.30.22      generics_0.1.3          
-##  [67] sp_2.1-2                 RCurl_1.98-1.13          ggplot2_3.4.4           
-##  [70] munsell_0.5.0            scales_1.3.0             xtable_1.8-4            
-##  [73] glue_1.6.2               tools_4.3.2              colourpicker_1.3.0      
-##  [76] locfit_1.5-9.8           fs_1.6.3                 rhdf5_2.46.1            
-##  [79] grid_4.3.2               colorspace_2.1-0         GenomeInfoDbData_1.2.11 
-##  [82] raster_3.6-26            beeswarm_0.4.0           HDF5Array_1.30.0        
-##  [85] vipor_0.4.7              cli_3.6.2                textshaping_0.3.7       
-##  [88] fansi_1.0.6              viridisLite_0.4.2        S4Arrays_1.2.0          
-##  [91] svglite_2.1.3            dplyr_1.1.4              gtable_0.3.4            
-##  [94] sass_0.4.8               digest_0.6.33            SparseArray_1.2.3       
-##  [97] rjson_0.2.21             htmlwidgets_1.6.4        memoise_2.0.1           
-## [100] htmltools_0.5.7          pkgdown_2.0.7            lifecycle_1.0.4         
-## [103] mime_0.12

+##   [7] compiler_4.4.1           png_0.1-8                systemfonts_1.1.0       
+##  [10] fftwtools_0.9-11         vctrs_0.6.5              pkgconfig_2.0.3         
+##  [13] SpatialExperiment_1.12.0 crayon_1.5.3             fastmap_1.2.0           
+##  [16] magick_2.8.3             XVector_0.42.0           fontawesome_0.5.2       
+##  [19] utf8_1.2.4               promises_1.3.0           rmarkdown_2.27          
+##  [22] ggbeeswarm_0.7.2         ragg_1.3.2               purrr_1.0.2             
+##  [25] xfun_0.45                zlibbioc_1.48.2          cachem_1.1.0            
+##  [28] jsonlite_1.8.8           later_1.3.2              rhdf5filters_1.14.1     
+##  [31] DelayedArray_0.28.0      Rhdf5lib_1.24.2          BiocParallel_1.36.0     
+##  [34] terra_1.7-78             jpeg_0.1-10              tiff_0.1-12             
+##  [37] parallel_4.4.1           R6_2.5.1                 bslib_0.7.0             
+##  [40] RColorBrewer_1.1-3       jquerylib_0.1.4          Rcpp_1.0.12             
+##  [43] bookdown_0.39            knitr_1.47               httpuv_1.6.15           
+##  [46] Matrix_1.7-0             nnls_1.5                 tidyselect_1.2.1        
+##  [49] viridis_0.6.5            abind_1.4-5              yaml_2.3.8              
+##  [52] codetools_0.2-20         miniUI_0.1.1.1           lattice_0.22-6          
+##  [55] tibble_3.2.1             shiny_1.8.1.1            evaluate_0.24.0         
+##  [58] archive_1.1.8            desc_1.4.3               shinycssloaders_1.0.0   
+##  [61] pillar_1.9.0             BiocManager_1.30.23      generics_0.1.3          
+##  [64] sp_2.1-4                 RCurl_1.98-1.14          ggplot2_3.5.1           
+##  [67] munsell_0.5.1            scales_1.3.0             xtable_1.8-4            
+##  [70] glue_1.7.0               tools_4.4.1              colourpicker_1.3.0      
+##  [73] locfit_1.5-9.10          fs_1.6.4                 rhdf5_2.46.1            
+##  [76] grid_4.4.1               colorspace_2.1-0         GenomeInfoDbData_1.2.11 
+##  [79] raster_3.6-26            beeswarm_0.4.0           HDF5Array_1.30.1        
+##  [82] vipor_0.4.7              cli_3.6.3                textshaping_0.4.0       
+##  [85] fansi_1.0.6              viridisLite_0.4.2        S4Arrays_1.2.1          
+##  [88] svglite_2.1.3            dplyr_1.1.4              gtable_0.3.5            
+##  [91] sass_0.4.9               digest_0.6.36            SparseArray_1.2.4       
+##  [94] rjson_0.2.21             htmlwidgets_1.6.4        memoise_2.0.1           
+##  [97] htmltools_0.5.8.1        pkgdown_2.0.9            lifecycle_1.0.4         
+## [100] mime_0.12

References

-
+
Angelo, Michael, Sean C. Bendall, Rachel Finck, Matthew B. Hale, Chuck Hitzman, Alexander D. Borowsky, Richard M. Levenson, et al. 2014. @@ -768,7 +775,7 @@

References

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/articles/index.html b/articles/index.html index 6e7f11d..e951caf 100644 --- a/articles/index.html +++ b/articles/index.html @@ -1,5 +1,5 @@ -Articles • cytoviewerArticles • cytoviewer @@ -17,7 +17,7 @@ cytoviewer - 1.3.3 + 1.5.0
@@ -62,7 +62,7 @@

All vignettes

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/authors.html b/authors.html index 76e0a5c..5a3eff5 100644 --- a/authors.html +++ b/authors.html @@ -1,5 +1,5 @@ -Authors and Citation • cytoviewerAuthors and Citation • cytoviewer @@ -17,7 +17,7 @@ cytoviewer - 1.3.3 + 1.5.0 @@ -44,7 +44,7 @@
-

Authors

+

Authors and Citation

@@ -85,7 +85,7 @@

Citation

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/index.html b/index.html index adfb164..4d5efd2 100644 --- a/index.html +++ b/index.html @@ -6,21 +6,13 @@ An interactive multi-channel image viewer for R • cytoviewer - + - + cytoviewer - Shiny application to interactively browse multi-channel images — cytoviewer • cytoviewercytoviewer - Shiny application to interactively browse multi-channel images — cytoviewer • cytoviewer cytoviewer - 1.3.3 + 1.5.0 @@ -182,8 +182,8 @@

Examples

#> as.data.frame, basename, cbind, colnames, dirname, do.call, #> duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, #> lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, -#> pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, -#> tapply, union, unique, unsplit, which.max, which.min +#> pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, +#> union, unique, unsplit, which.max, which.min #> #> Attaching package: ‘S4Vectors’ #> The following object is masked from ‘package:utils’: @@ -272,7 +272,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/reference/index.html b/reference/index.html index d46b7fe..c130a4e 100644 --- a/reference/index.html +++ b/reference/index.html @@ -1,5 +1,5 @@ -Function reference • cytoviewerFunction reference • cytoviewer @@ -17,7 +17,7 @@ cytoviewer - 1.3.3 + 1.5.0 @@ -67,7 +67,7 @@

All functions
-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.