diff --git a/404.html b/404.html index ba52ef53..dcc970a3 100644 --- a/404.html +++ b/404.html @@ -26,7 +26,7 @@ - +
- +
@@ -117,16 +117,16 @@

Page not found (404)

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html index 5ce56300..18992178 100644 --- a/CODE_OF_CONDUCT.html +++ b/CODE_OF_CONDUCT.html @@ -3,7 +3,7 @@ - +
- +
@@ -148,15 +148,15 @@

Attribution -

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/CONTRIBUTING.html b/CONTRIBUTING.html index f0175073..108ead1f 100644 --- a/CONTRIBUTING.html +++ b/CONTRIBUTING.html @@ -3,7 +3,7 @@ - +
- +
@@ -111,15 +111,15 @@

Code of Conduct
-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/SUPPORT.html b/SUPPORT.html index 7451dbb4..d55046f9 100644 --- a/SUPPORT.html +++ b/SUPPORT.html @@ -3,7 +3,7 @@ - +
- +
@@ -109,15 +109,15 @@

What happens next? -

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/articles/TenX_data_download.html b/articles/TenX_data_download.html index 3cdb1df7..97c9b7d5 100644 --- a/articles/TenX_data_download.html +++ b/articles/TenX_data_download.html @@ -19,15 +19,13 @@ - - - +
- +
@@ -262,6 +260,8 @@

Load packages## Load packages in the order we'll use them next library("BiocFileCache") library("SpatialExperiment") +#> Warning: package 'S4Vectors' was built under R version 4.4.1 +#> Warning: package 'IRanges' was built under R version 4.4.1 library("rtracklayer") library("lobstr") library("spatialLIBD")

@@ -311,9 +311,8 @@

Download spaceranger output files#> V1_Human_Lymph_Node_spatial.tar.gz.BFC21 #> 0 #> V1_Human_Lymph_Node_analysis.tar.gz.BFC22 -#> 0

-
-
+#>                                                           0
+
 ## List the files we downloaded and extracted
 ## These files are typically SpaceRanger outputs
 lymph.dirs <- file.path(
@@ -337,7 +336,7 @@ 
Download spaceranger output filestype = "sparse" argument to load the data into an R object
 that is memory-efficient for sparse data.

-
+
 ## Import the data as a SpatialExperiment object
 spe <- SpatialExperiment::read10xVisium(
     samples = tempdir(),
@@ -350,12 +349,10 @@ 
Download spaceranger output filesclass(spe)
 #> [1] "SpatialExperiment"
 #> attr(,"package")
-#> [1] "SpatialExperiment"

-
-lobstr::obj_size(spe) / 1024^2 ## Convert to MB
-#> 281.90 B

-
-spe
+#> [1] "SpatialExperiment"
+lobstr::obj_size(spe) / 1024^2 ## Convert to MB
+#> 281.90 B
+spe
 #> class: SpatialExperiment 
 #> dim: 36601 4035 
 #> metadata(0):
@@ -370,9 +367,8 @@ 
Download spaceranger output files#> mainExpName: NULL
 #> altExpNames(0):
 #> spatialCoords names(2) : pxl_col_in_fullres pxl_row_in_fullres
-#> imgData names(4): sample_id image_id data scaleFactor

-
-
+#> imgData names(4): sample_id image_id data scaleFactor
+
 ## The counts are saved in a sparse matrix R object
 class(counts(spe))
 #> [1] "dgCMatrix"
@@ -404,7 +400,7 @@ 
Modify spe for spatialLIBDsum_gene: this continuous variable contains the number
 of genes that have at least 1 count.
 
-
+
 ## Add some information used by spatialLIBD
 spe <- add_key(spe)
 spe$sum_umi <- colSums(counts(spe))
@@ -423,7 +419,7 @@ 
Add gene annotation information
-
+
 ## Initially we don't have much information about the genes
 rowRanges(spe)
 #> GRangesList object of length 36601:
@@ -466,14 +462,14 @@ 
From 10xSpatialExperiment::read10xVisium() does not include.

 
For example, in our computing cluster this GTF file is located at the
 following path and is 1.4 GB in size:

-
$ cd /dcs04/lieber/lcolladotor/annotationFiles_LIBD001/10x/refdata-gex-GRCh38-2020-A
-$ du -sh --apparent-size genes/genes.gtf
-1.4G    genes/genes.gtf

+
$ cd /dcs04/lieber/lcolladotor/annotationFiles_LIBD001/10x/refdata-gex-GRCh38-2020-A
+$ du -sh --apparent-size genes/genes.gtf
+1.4G    genes/genes.gtf

 
If you have the GTF file from 10x Genomics, we show next how you can
 read the information into R, match it appropriately with the information
 in the spe object and add it back into the spe
 object.

-
+
 ## You could:
 ## * download the 11 GB file from
 ## https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38-2020-A.tar.gz
@@ -525,7 +521,7 @@ 
From Gencode
+
-
-
-
+#> 36572    29
+
 ## Drop the few genes for which we don't have information
 spe <- spe[!is.na(match_genes), ]
 match_genes <- match_genes[!is.na(match_genes)]
@@ -621,7 +615,7 @@ 

@@ -254,15 +254,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/vis_grid_gene.html b/reference/vis_grid_gene.html
index 318ec40c..f5428110 100644
--- a/reference/vis_grid_gene.html
+++ b/reference/vis_grid_gene.html
@@ -6,7 +6,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

@@ -104,51 +104,53 @@ 
Sample spatial gene visualization grid

 
     

     
Arguments

-    
spe

-
Defaults to the output of
-fetch_data(type = 'spe'). This is a
+
+
+
spe

+
A
 SpatialExperiment-class
-object with the spot-level Visium data and information required for
-visualizing the histology. See fetch_data() for more details.

+object. See fetch_data() for how to download some example objects or
+read10xVisiumWrapper() to read in spaceranger --count output files and
+build your own spe object.

 
 
-
geneid

+
geneid

 
A character() specifying the gene ID(s) stored in
-rowData(spe)$gene_search or a continuous variable(s) stored in colData(spe)
-to visualize. For each ID, if rowData(spe)$gene_search is missing, then
-rownames(spe) is used to search for the gene ID. When a vector of length > 1
-is supplied, the continuous variables are combined according to multi_gene_method,
-producing a single value for each spot.

+rowData(spe)$gene_search or a continuous variable(s) stored in
+colData(spe) to visualize. For each ID, if rowData(spe)$gene_search is
+missing, then rownames(spe) is used to search for the gene ID. When a
+vector of length > 1 is supplied, the continuous variables are combined
+according to multi_gene_method, producing a single value for each spot.

 
 
-
pdf_file

+
pdf_file

 
A character(1) specifying the path for the resulting PDF.

 
 
-
assayname

+
assayname

 
The name of the assays(spe) to use for extracting the
 gene expression data. Defaults to logcounts.

 
 
-
minCount

+
minCount

 
A numeric(1) specifying the minimum gene expression (or
 value in the continuous variable) to visualize. Values at or below this
 threshold will be set to NA. Defaults to 0.

 
 
-
return_plots

+
return_plots

 
A logical(1) indicating whether to print the plots
 to a PDF or to return the list of plots that you can then print using
 plot_grid.

 
 
-
spatial

+
spatial

 
A logical(1) indicating whether to include the histology
 layer from geom_spatial(). If you plan to use
 ggplotly() then it's best to set this to FALSE.

 
 
-
viridis

+
viridis

 
A logical(1) whether to use the color-blind friendly
 palette from viridis or the color palette used
 in the paper that was chosen for contrast when visualizing the data on
@@ -157,46 +159,46 @@ 
Arguments

 dependent on cell density.

 
 
-
height

+
height

 
A numeric(1) passed to pdf.

 
 
-
width

+
width

 
A numeric(1) passed to pdf.

 
 
-
image_id

+
image_id

 
A character(1) with the name of the image ID you want to
 use in the background.

 
 
-
alpha

+
alpha

 
A numeric(1) in the [0, 1] range that specifies the
 transparency level of the data on the spots.

 
 
-
cont_colors

+
cont_colors

 
A character() vector of colors that supersedes the
 viridis argument.

 
 
-
sample_order

+
sample_order

 
A character() with the names of the samples to use
 and their order.

 
 
-
point_size

+
point_size

 
A numeric(1) specifying the size of the points. Defaults
 to 1.25. Some colors look better if you use 2 for instance.

 
 
-
auto_crop

+
auto_crop

 
A logical(1) indicating whether to automatically crop
 the image / plotting area, which is useful if the Visium capture area is
 not centered on the image and if the image is not a square.

 
 
-
na_color

+
na_color

 
A character(1) specifying a color for the NA values.
 If you set alpha = NA then it's best to set na_color to a color that has
 alpha blending already, which will make non-NA values pop up more and the NA
@@ -204,7 +206,7 @@ 
Arguments

 set to a non-NA value.

 
 
-
is_stitched

+
is_stitched

 
A logical(1) vector: If TRUE, expects a
 SpatialExperiment-class built
 with visiumStitched::build_spe().
@@ -213,16 +215,14 @@ 
Arguments

 specifying which spots to exclude from the plot. Sets auto_crop = FALSE.

 
 
-
...

+
...

 
Passed to paste0() for making the title of the
 plot following the sampleid.

 
 

     

     
Value

-    
-
-
A list of ggplot2 objects.

+    
A list of ggplot2 objects.

     

     

     
Details

@@ -232,9 +232,9 @@ 
Details

     

     

     
See also

-    
Other Spatial gene visualization functions: 
+    
Other Spatial gene visualization functions:
 vis_gene(),
-vis_gene_p()

+vis_gene_p()

     

 
     

@@ -257,7 +257,7 @@ 
Examples

     cowplot::plot_grid(plotlist = p_list, ncol = 2)
 }
 #> snapshotDate(): 2024-04-29
-#> 2024-07-16 11:35:26.639962 loading file /Users/leocollado/Library/Caches/org.R-project.R/R/BiocFileCache/6f56656adcb_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-16 17:03:53.38865 loading file /Users/leocollado/Library/Caches/org.R-project.R/R/BiocFileCache/6f56656adcb_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 
 

     

@@ -273,15 +273,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/sitemap.xml b/sitemap.xml
index 6303d1f9..d4f77066 100644
--- a/sitemap.xml
+++ b/sitemap.xml
@@ -1,201 +1,68 @@
-
-
-  
-    /404.html
-  
-  
-    /CODE_OF_CONDUCT.html
-  
-  
-    /CONTRIBUTING.html
-  
-  
-    /SUPPORT.html
-  
-  
-    /articles/TenX_data_download.html
-  
-  
-    /articles/guide_to_spatial_registration.html
-  
-  
-    /articles/index.html
-  
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-  
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-  
-  
-    /authors.html
-  
-  
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-  
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-  
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-  
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-  
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-    /reference/multi_gene_pca.html
-  
-  
-    /reference/multi_gene_sparsity.html
-  
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-    /reference/multi_gene_z_score.html
-  
-  
-    /reference/prep_stitched_data.html
-  
-  
-    /reference/read10xVisiumAnalysis.html
-  
-  
-    /reference/read10xVisiumWrapper.html
-  
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-    /reference/registration_block_cor.html
-  
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-    /reference/registration_model.html
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-  
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-  
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-  
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-    /reference/sort_clusters.html
-  
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-    /reference/spatialLIBD-package.html
-  
-  
-    /reference/tstats_Human_DLPFC_snRNAseq_Nguyen_topLayer.html
-  
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-  
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-  
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-    /reference/vis_grid_clus.html
-  
-  
-    /reference/vis_grid_gene.html
-  
+
+/404.html
+/CODE_OF_CONDUCT.html
+/CONTRIBUTING.html
+/SUPPORT.html
+/articles/TenX_data_download.html
+/articles/guide_to_spatial_registration.html
+/articles/index.html
+/articles/multi_gene_plots.html
+/articles/spatialLIBD.html
+/authors.html
+/index.html
+/news/index.html
+/reference/add10xVisiumAnalysis.html
+/reference/add_images.html
+/reference/add_key.html
+/reference/add_qc_metrics.html
+/reference/annotate_registered_clusters.html
+/reference/check_modeling_results.html
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+/reference/cluster_export.html
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+/reference/enough_ram.html
+/reference/fetch_data.html
+/reference/frame_limits.html
+/reference/gene_set_enrichment.html
+/reference/gene_set_enrichment_plot.html
+/reference/geom_spatial.html
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+/reference/img_edit.html
+/reference/img_update.html
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+/reference/layer_matrix_plot.html
+/reference/layer_stat_cor.html
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+/reference/locate_images.html
+/reference/multi_gene_pca.html
+/reference/multi_gene_sparsity.html
+/reference/multi_gene_z_score.html
+/reference/prep_stitched_data.html
+/reference/read10xVisiumAnalysis.html
+/reference/read10xVisiumWrapper.html
+/reference/registration_block_cor.html
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+/reference/registration_pseudobulk.html
+/reference/registration_stats_anova.html
+/reference/registration_stats_enrichment.html
+/reference/registration_stats_pairwise.html
+/reference/registration_wrapper.html
+/reference/run_app.html
+/reference/sce_to_spe.html
+/reference/sig_genes_extract.html
+/reference/sig_genes_extract_all.html
+/reference/sort_clusters.html
+/reference/spatialLIBD-package.html
+/reference/tstats_Human_DLPFC_snRNAseq_Nguyen_topLayer.html
+/reference/vis_clus.html
+/reference/vis_clus_p.html
+/reference/vis_gene.html
+/reference/vis_grid_clus.html
+/reference/vis_grid_gene.html
 
+