From 4a681234796a887c1858cd865d98a541863e6c88 Mon Sep 17 00:00:00 2001 From: stemangiola Date: Thu, 19 Dec 2024 23:40:02 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20stemangi?= =?UTF-8?q?ola/tidySingleCellExperiment@61477f1a1aa5658ffdbd296b6ab5bf9e02?= =?UTF-8?q?c18b92=20=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- articles/introduction.html | 4 ++-- authors.html | 2 +- index.html | 6 +++++- pkgdown.yml | 2 +- reference/add_class.html | 2 +- reference/aggregate_cells.html | 2 +- reference/anti_join.html | 2 +- reference/arrange.html | 2 +- reference/as_tibble.html | 2 +- reference/bind_rows.html | 2 +- reference/cell_type_df.html | 2 +- reference/count.html | 2 +- reference/distinct.html | 2 +- reference/drop_class.html | 2 +- reference/extract.html | 2 +- reference/filter.html | 2 +- reference/formatting.html | 2 +- reference/full_join.html | 2 +- reference/ggplot.html | 2 +- reference/glimpse.html | 2 +- reference/group_by.html | 2 +- reference/group_split.html | 2 +- reference/inner_join.html | 2 +- reference/join_features.html | 2 +- reference/join_transcripts.html | 2 +- reference/left_join.html | 2 +- reference/mutate.html | 2 +- reference/nest.html | 2 +- reference/pbmc_small.html | 2 +- reference/pbmc_small_nested_interactions.html | 2 +- reference/pipe.html | 2 +- reference/pivot_longer.html | 2 +- reference/plot_ly.html | 4 ++-- reference/pull.html | 2 +- reference/quo_names.html | 2 +- reference/rename.html | 2 +- reference/return_arguments_of.html | 2 +- reference/right_join.html | 2 +- reference/rowwise.html | 2 +- reference/sample_n.html | 2 +- reference/select.html | 2 +- reference/separate.html | 2 +- reference/slice.html | 2 +- reference/summarise.html | 2 +- reference/tbl_format_header.html | 2 +- reference/tidy.html | 2 +- reference/unite.html | 2 +- reference/unnest.html | 2 +- 48 files changed, 54 insertions(+), 50 deletions(-) diff --git a/articles/introduction.html b/articles/introduction.html index b3e11bb..e4e74c8 100644 --- a/articles/introduction.html +++ b/articles/introduction.html @@ -80,7 +80,7 @@

Stefano Mangiola

- Source: vignettes/introduction.Rmd + Source: vignettes/introduction.Rmd @@ -754,7 +754,7 @@

Session Info
 sessionInfo()
-
## R Under development (unstable) (2024-12-15 r87442)
+
## R Under development (unstable) (2024-12-17 r87446)
 ## Platform: x86_64-pc-linux-gnu
 ## Running under: Ubuntu 24.04.1 LTS
 ## 
diff --git a/authors.html b/authors.html
index 2362636..dd9e756 100644
--- a/authors.html
+++ b/authors.html
@@ -63,7 +63,7 @@ 
Authors and Citation

     

     

       
Citation

-      Source: DESCRIPTION
+      Source: DESCRIPTION
     

     

 
diff --git a/index.html b/index.html
index b91c06e..09b7b40 100644
--- a/index.html
+++ b/index.html
@@ -383,7 +383,11 @@ 
Preprocess the dataset
 ## Warning in (function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth =
 ## TRUE, : You're computing too large a percentage of total singular values, use a
-## standard svd instead.

+## standard svd instead.
+
+## Warning in (function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth =
+## TRUE, : did not converge--results might be invalid!; try increasing work or
+## maxit
 pbmc_small_pca
## [90m# A SingleCellExperiment-tibble abstraction: 80 × 18[39m
diff --git a/pkgdown.yml b/pkgdown.yml
index 6ec92f2..77e8f15 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,4 +3,4 @@ pkgdown: 2.1.1
 pkgdown_sha: ~
 articles:
   introduction: introduction.html
-last_built: 2024-12-19T14:17Z
+last_built: 2024-12-19T23:38Z
diff --git a/reference/add_class.html b/reference/add_class.html
index f23c6a6..cd150cb 100644
--- a/reference/add_class.html
+++ b/reference/add_class.html
@@ -51,7 +51,7 @@
   

     

     
Add class to abject

-    Source: R/utilities.R
+    Source: R/utilities.R
     
     

 
diff --git a/reference/aggregate_cells.html b/reference/aggregate_cells.html
index e7fac3e..1f250a6 100644
--- a/reference/aggregate_cells.html
+++ b/reference/aggregate_cells.html
@@ -51,7 +51,7 @@
   

     

     
Aggregate cells

-    Source: R/methods.R
+    Source: R/methods.R
     
     

 
diff --git a/reference/anti_join.html b/reference/anti_join.html
index a2bd7f9..879988c 100644
--- a/reference/anti_join.html
+++ b/reference/anti_join.html
@@ -56,7 +56,7 @@
   

     

     
Filtering joins

-    Source: R/dplyr_methods.R
+    Source: R/dplyr_methods.R
     
     

 
diff --git a/reference/arrange.html b/reference/arrange.html
index 0eba030..d7fcd7a 100644
--- a/reference/arrange.html
+++ b/reference/arrange.html
@@ -56,7 +56,7 @@
   

     

     
Order rows using column values

-    Source: R/dplyr_methods.R
+    Source: R/dplyr_methods.R
     
     

 
diff --git a/reference/as_tibble.html b/reference/as_tibble.html
index 323bd56..06968a7 100644
--- a/reference/as_tibble.html
+++ b/reference/as_tibble.html
@@ -66,7 +66,7 @@
   

     

     
Coerce lists, matrices, and more to data frames

-    Source: R/tibble_methods.R
+    Source: R/tibble_methods.R
     
     

 
diff --git a/reference/bind_rows.html b/reference/bind_rows.html
index 6a9920e..34b0f3c 100644
--- a/reference/bind_rows.html
+++ b/reference/bind_rows.html
@@ -56,7 +56,7 @@
   

     

     
Efficiently bind multiple data frames by row and column

-    Source: R/dplyr_methods.R
+    Source: R/dplyr_methods.R
     
     

 
diff --git a/reference/cell_type_df.html b/reference/cell_type_df.html
index 1526a1b..547555c 100644
--- a/reference/cell_type_df.html
+++ b/reference/cell_type_df.html
@@ -51,7 +51,7 @@
   

     

     
Cell types of 80 PBMC single cells

-    Source: R/data.R
+    Source: R/data.R
     
     

 
diff --git a/reference/count.html b/reference/count.html
index 4f2b79b..7b7ca57 100644
--- a/reference/count.html
+++ b/reference/count.html
@@ -59,7 +59,7 @@
   

     

     
Count the observations in each group

-    Source: R/dplyr_methods.R
+    Source: R/dplyr_methods.R
     
     

 
diff --git a/reference/distinct.html b/reference/distinct.html
index ec99c19..eb8b4c1 100644
--- a/reference/distinct.html
+++ b/reference/distinct.html
@@ -52,7 +52,7 @@
   

     

     
Keep distinct/unique rows

-    Source: R/dplyr_methods.R
+    Source: R/dplyr_methods.R
     
     

 
diff --git a/reference/drop_class.html b/reference/drop_class.html
index 6ab8548..8bbfd83 100644
--- a/reference/drop_class.html
+++ b/reference/drop_class.html
@@ -51,7 +51,7 @@
   

     

     
Remove class to abject

-    Source: R/utilities.R
+    Source: R/utilities.R
     
     

 
diff --git a/reference/extract.html b/reference/extract.html
index 3a44b78..bba5dc4 100644
--- a/reference/extract.html
+++ b/reference/extract.html
@@ -58,7 +58,7 @@
   

     

     
Extract a character column into multiple columns using regular expression groups

-    Source: R/tidyr_methods.R
+    Source: R/tidyr_methods.R
     
     

 
diff --git a/reference/filter.html b/reference/filter.html
index d398cfc..a288867 100644
--- a/reference/filter.html
+++ b/reference/filter.html
@@ -55,7 +55,7 @@
   

     

     
Keep rows that match a condition

-    Source: R/dplyr_methods.R
+    Source: R/dplyr_methods.R
     
     

 
diff --git a/reference/formatting.html b/reference/formatting.html
index 0b0f6c8..dae2aa5 100644
--- a/reference/formatting.html
+++ b/reference/formatting.html
@@ -70,7 +70,7 @@
   

     

     
Printing tibbles

-    Source: R/print_method.R
+    Source: R/print_method.R
     
     

 
diff --git a/reference/full_join.html b/reference/full_join.html
index 3861b7b..a713b84 100644
--- a/reference/full_join.html
+++ b/reference/full_join.html
@@ -77,7 +77,7 @@
   

     

     
Mutating joins

-    Source: R/dplyr_methods.R
+    Source: R/dplyr_methods.R
     
     

 
diff --git a/reference/ggplot.html b/reference/ggplot.html
index 547276c..b1ef06c 100644
--- a/reference/ggplot.html
+++ b/reference/ggplot.html
@@ -54,7 +54,7 @@
   

     

     
Create a new ggplot from a tidySingleCellExperiment

-    Source: R/ggplot2_methods.R
+    Source: R/ggplot2_methods.R
     
     

 
diff --git a/reference/glimpse.html b/reference/glimpse.html
index 4e76df4..4d46539 100644
--- a/reference/glimpse.html
+++ b/reference/glimpse.html
@@ -58,7 +58,7 @@
   

     

     
Get a glimpse of your data

-    Source: R/tibble_methods.R
+    Source: R/tibble_methods.R
     
     

 
diff --git a/reference/group_by.html b/reference/group_by.html
index 3735cde..cf6885c 100644
--- a/reference/group_by.html
+++ b/reference/group_by.html
@@ -53,7 +53,7 @@
   

     

     
Group by one or more variables

-    Source: R/dplyr_methods.R
+    Source: R/dplyr_methods.R
     
     

 
diff --git a/reference/group_split.html b/reference/group_split.html
index 15446c0..2fddf9c 100644
--- a/reference/group_split.html
+++ b/reference/group_split.html
@@ -63,7 +63,7 @@
   

     

     
Split data frame by groups

-    Source: R/dplyr_methods.R
+    Source: R/dplyr_methods.R
     
     

 
diff --git a/reference/inner_join.html b/reference/inner_join.html
index 2189523..5dc8f0e 100644
--- a/reference/inner_join.html
+++ b/reference/inner_join.html
@@ -77,7 +77,7 @@
   

     

     
Mutating joins

-    Source: R/dplyr_methods.R
+    Source: R/dplyr_methods.R
     
     

 
diff --git a/reference/join_features.html b/reference/join_features.html
index aa114e0..78f8e26 100644
--- a/reference/join_features.html
+++ b/reference/join_features.html
@@ -52,7 +52,7 @@
   

     

     
join_features

-    Source: R/methods.R
+    Source: R/methods.R
     
     

 
diff --git a/reference/join_transcripts.html b/reference/join_transcripts.html
index 3479383..5ecc8d7 100644
--- a/reference/join_transcripts.html
+++ b/reference/join_transcripts.html
@@ -51,7 +51,7 @@
   

     

     
(DEPRECATED) Extract and join information for transcripts.

-    Source: R/methods_DEPRECATED.R
+    Source: R/methods_DEPRECATED.R
     
     

 
diff --git a/reference/left_join.html b/reference/left_join.html
index fd2eaaa..040d1d1 100644
--- a/reference/left_join.html
+++ b/reference/left_join.html
@@ -77,7 +77,7 @@
   

     

     
Mutating joins

-    Source: R/dplyr_methods.R
+    Source: R/dplyr_methods.R
     
     

 
diff --git a/reference/mutate.html b/reference/mutate.html
index dd0370f..2c97749 100644
--- a/reference/mutate.html
+++ b/reference/mutate.html
@@ -53,7 +53,7 @@
   

     

     
Create, modify, and delete columns

-    Source: R/dplyr_methods.R
+    Source: R/dplyr_methods.R
     
     

 
diff --git a/reference/nest.html b/reference/nest.html
index eafd318..b4d8293 100644
--- a/reference/nest.html
+++ b/reference/nest.html
@@ -56,7 +56,7 @@
   

     

     
Nest rows into a list-column of data frames

-    Source: R/tidyr_methods.R
+    Source: R/tidyr_methods.R
     
     

 
diff --git a/reference/pbmc_small.html b/reference/pbmc_small.html
index b0f045c..aa742d0 100644
--- a/reference/pbmc_small.html
+++ b/reference/pbmc_small.html
@@ -51,7 +51,7 @@
   

     

     
pbmc_small

-    Source: R/data.R
+    Source: R/data.R
     
     

 
diff --git a/reference/pbmc_small_nested_interactions.html b/reference/pbmc_small_nested_interactions.html
index 5d5a49d..2439da0 100644
--- a/reference/pbmc_small_nested_interactions.html
+++ b/reference/pbmc_small_nested_interactions.html
@@ -53,7 +53,7 @@
   

     

     
Intercellular ligand-receptor interactions for 38 ligands from a single cell RNA-seq cluster.

-    Source: R/data.R
+    Source: R/data.R
     
     

 
diff --git a/reference/pipe.html b/reference/pipe.html
index 83ad033..1395673 100644
--- a/reference/pipe.html
+++ b/reference/pipe.html
@@ -51,7 +51,7 @@
   

     

     
Pipe operator

-    Source: R/utils-pipe.R
+    Source: R/utils-pipe.R
     
     

 
diff --git a/reference/pivot_longer.html b/reference/pivot_longer.html
index 8dea802..fb693eb 100644
--- a/reference/pivot_longer.html
+++ b/reference/pivot_longer.html
@@ -54,7 +54,7 @@
   

     

     
Pivot data from wide to long

-    Source: R/tidyr_methods.R
+    Source: R/tidyr_methods.R
     
     

 
diff --git a/reference/plot_ly.html b/reference/plot_ly.html
index fc1ca78..7ae302e 100644
--- a/reference/plot_ly.html
+++ b/reference/plot_ly.html
@@ -56,7 +56,7 @@
   

     

     
Initiate a plotly visualization

-    Source: R/plotly_methods.R
+    Source: R/plotly_methods.R
     
     

 
@@ -274,7 +274,7 @@ 
Examples

 pbmc_small |> 
     plot_ly(x = ~ nCount_RNA, y = ~ nFeature_RNA)
 

-
+
diff --git a/reference/pull.html b/reference/pull.html index f527312..4b69061 100644 --- a/reference/pull.html +++ b/reference/pull.html @@ -53,7 +53,7 @@

Extract a single column

- Source: R/dplyr_methods.R + Source: R/dplyr_methods.R
diff --git a/reference/quo_names.html b/reference/quo_names.html index 0b8e7c8..0f9213a 100644 --- a/reference/quo_names.html +++ b/reference/quo_names.html @@ -51,7 +51,7 @@

Convert array of quosure (e.g. c(col_a, col_b)) into character vector

- Source: R/utilities.R + Source: R/utilities.R
diff --git a/reference/rename.html b/reference/rename.html index d45e6cf..6d10c50 100644 --- a/reference/rename.html +++ b/reference/rename.html @@ -53,7 +53,7 @@

Rename columns

- Source: R/dplyr_methods.R + Source: R/dplyr_methods.R
diff --git a/reference/return_arguments_of.html b/reference/return_arguments_of.html index 168e0ff..1d53d78 100644 --- a/reference/return_arguments_of.html +++ b/reference/return_arguments_of.html @@ -51,7 +51,7 @@

returns variables from an expression

- Source: R/utilities.R + Source: R/utilities.R
diff --git a/reference/right_join.html b/reference/right_join.html index e5e3d8d..ce3c1f3 100644 --- a/reference/right_join.html +++ b/reference/right_join.html @@ -77,7 +77,7 @@

Mutating joins

- Source: R/dplyr_methods.R + Source: R/dplyr_methods.R
diff --git a/reference/rowwise.html b/reference/rowwise.html index 5ac14a4..4ebd950 100644 --- a/reference/rowwise.html +++ b/reference/rowwise.html @@ -55,7 +55,7 @@

Group input by rows

- Source: R/dplyr_methods.R + Source: R/dplyr_methods.R
diff --git a/reference/sample_n.html b/reference/sample_n.html index f18e5d1..dc1d9bb 100644 --- a/reference/sample_n.html +++ b/reference/sample_n.html @@ -68,7 +68,7 @@

Sample n rows from a table

- Source: R/dplyr_methods.R + Source: R/dplyr_methods.R
diff --git a/reference/select.html b/reference/select.html index 0f25a28..d242559 100644 --- a/reference/select.html +++ b/reference/select.html @@ -96,7 +96,7 @@

Keep or drop columns using their names and types

- Source: R/dplyr_methods.R + Source: R/dplyr_methods.R
diff --git a/reference/separate.html b/reference/separate.html index 20ab40d..ef1d0f4 100644 --- a/reference/separate.html +++ b/reference/separate.html @@ -58,7 +58,7 @@

Separate a character column into multiple columns with a regular expression or numeric locations

- Source: R/tidyr_methods.R + Source: R/tidyr_methods.R
diff --git a/reference/slice.html b/reference/slice.html index 72fb48b..0fe40a6 100644 --- a/reference/slice.html +++ b/reference/slice.html @@ -62,7 +62,7 @@

Subset rows using their positions

- Source: R/dplyr_methods.R + Source: R/dplyr_methods.R
diff --git a/reference/summarise.html b/reference/summarise.html index ef214a3..d700766 100644 --- a/reference/summarise.html +++ b/reference/summarise.html @@ -56,7 +56,7 @@

Summarise each group down to one row

- Source: R/dplyr_methods.R + Source: R/dplyr_methods.R
diff --git a/reference/tbl_format_header.html b/reference/tbl_format_header.html index a5f82e5..88e3008 100644 --- a/reference/tbl_format_header.html +++ b/reference/tbl_format_header.html @@ -60,7 +60,7 @@

Format the header of a tibble

- Source: R/print_method.R + Source: R/print_method.R
diff --git a/reference/tidy.html b/reference/tidy.html index 27ea3a6..f5a9c68 100644 --- a/reference/tidy.html +++ b/reference/tidy.html @@ -51,7 +51,7 @@

tidy for `SingleCellExperiment`

- Source: R/methods.R + Source: R/methods.R
diff --git a/reference/unite.html b/reference/unite.html index 173a771..588d957 100644 --- a/reference/unite.html +++ b/reference/unite.html @@ -51,7 +51,7 @@

Unite multiple columns into one by pasting strings together

- Source: R/tidyr_methods.R + Source: R/tidyr_methods.R
diff --git a/reference/unnest.html b/reference/unnest.html index 6a8d7e2..12b09dc 100644 --- a/reference/unnest.html +++ b/reference/unnest.html @@ -51,7 +51,7 @@

Unnest a list-column of data frames into rows and columns

- Source: R/tidyr_methods.R + Source: R/tidyr_methods.R