From e00b6602eb7de9bcc8b1b2a1846cbee17f841487 Mon Sep 17 00:00:00 2001 From: LTLA Date: Wed, 4 Dec 2024 19:19:19 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20kanavers?= =?UTF-8?q?e/wobbegong-R@629bf6e80ba62312e83f34de8affd09bbe7be0f3=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- 404.html | 2 +- LICENSE-text.html | 2 +- authors.html | 6 ++--- index.html | 18 ++++++++++--- pkgdown.yml | 2 +- reference/index.html | 4 +-- reference/wobbegongify.html | 51 +++++++++++++++++++++++++++++++------ 7 files changed, 65 insertions(+), 20 deletions(-) diff --git a/404.html b/404.html index f1688a5..ab39160 100644 --- a/404.html +++ b/404.html @@ -32,7 +32,7 @@ wobbegong - 0.2.0 + 0.2.1 diff --git a/LICENSE-text.html b/LICENSE-text.html index d1fe43f..19815ed 100644 --- a/LICENSE-text.html +++ b/LICENSE-text.html @@ -17,7 +17,7 @@ wobbegong - 0.2.0 + 0.2.1 diff --git a/authors.html b/authors.html index 71251d7..ad259ed 100644 --- a/authors.html +++ b/authors.html @@ -17,7 +17,7 @@ wobbegong - 0.2.0 + 0.2.1 @@ -54,13 +54,13 @@

Citation

Lun A (2024). wobbegong: Cheap-ass Range Requests on Assay Data. -R package version 0.2.0. +R package version 0.2.1. 

@Manual{,
   title = {wobbegong: Cheap-ass Range Requests on Assay Data},
   author = {Aaron Lun},
   year = {2024},
-  note = {R package version 0.2.0},
+  note = {R package version 0.2.1},
 }
diff --git a/index.html b/index.html index fe16472..f8183d6 100644 --- a/index.html +++ b/index.html @@ -33,7 +33,7 @@ wobbegong - 0.2.0 + 0.2.1 @@ -75,8 +75,12 @@

Quick startwobbegongify() function on our SummarizedExperiment of interest:

 library(wobbegong)
-wobbegongify(my_se, "/my/server/directory")
-

This will dump a whole bunch of files at the specified directory, which can be accessed with wobbegong.js.

+wobbegongify(my_se, "/my/server/directory/se") +

This will dump a whole bunch of files at the specified directory, which can be accessed with wobbegong.js. We can also directly wobbegongify() a DataFrame:

+
+library(S4Vectors)
+my_df <- DataFrame(a = 1:5, b = LETTERS[1:5])
+wobbegongify(my_df, "/my/server/directory/df")

Check out the reference documentation for more details.

@@ -88,6 +92,8 @@

For a SummarizedExperimentThe top-level directory (referred to here as {DIR}) has a number of files and subdirectories. The most important is {DIR}/summary.json, which provides a summary of the SummarizedExperiment’s components. This will have the following properties:

If has_row_data = true, a {DIR}/row_data subdirectory will be present, containing the row annotations in the DataFrame directory layout.

If has_column_data = true, a {DIR}/column_data subdirectory will be present, containing the column annotations in the DataFrame directory layout.

@@ -112,6 +118,8 @@

For a DataFrameEach DataFrame directory contains a summary.json file and a content file. The summary.json file has the following properties:

@@ -44,7 +44,7 @@

All functions

wobbegongify()

-

Dump a SummarizedExperiment to disk

+

Convert an object to the wobbegong format

@@ -34,17 +34,26 @@
-

Dump a SummarizedExperiment to disk

+

Convert an object to the wobbegong format

-

Dump a SummarizedExperiment (or one of its subclasses) to disk in the wobbegong format for easy HTTP range requests.

+

Dump an object to disk in the wobbegong format for easy HTTP range requests.

- 
wobbegongify(x, path, dense.assays = TRUE, sparse.assays = TRUE)
+ 
wobbegongify(x, path, ...)
+
+# S4 method for class 'SummarizedExperiment'
+wobbegongify(x, path, dense.assays = TRUE, sparse.assays = TRUE, ...)
+
+# S4 method for class 'SingleCellExperiment'
+wobbegongify(x, path, dense.assays = TRUE, sparse.assays = TRUE, ...)
+
+# S4 method for class 'DataFrame'
+wobbegongify(x, path, ...)
@@ -52,13 +61,17 @@

Arguments

x
-

A SummarizedExperiment or an instance of one of its subclasses.

+

A supported R object, typically a SummarizedExperiment or an instance of one of its subclasses.

path

String containing a path to the directory to dump x.

+
...
+

Additional arguments for specific methods.

+ +
dense.assays

Logical scalar indicating whether to save dense assays. If FALSE, dense assays are skipped.

@@ -157,11 +170,11 @@

Examples

counts=matrix(rpois(200, lambda=5), ncol=10), logcounts=matrix(rnorm(200), ncol=10) ), - colData = DataFrame( + colData = DataFrame( yy = letters[1:10], xx = LETTERS[1:10] ), - rowData = DataFrame(row.names=sprintf("GENE_%i", 1:20)), + rowData = DataFrame(row.names=sprintf("GENE_%i", 1:20)), reducedDims = list( PCA = matrix(rnorm(50), nrow=10), TSNE = matrix(rnorm(20), nrow=10) @@ -170,6 +183,27 @@

Examples

tmp <- tempfile() wobbegongify(se, tmp) +#> $object +#> [1] "summarized_experiment" +#> +#> $row_count +#> [1] 20 +#> +#> $column_count +#> [1] 10 +#> +#> $has_row_data +#> [1] TRUE +#> +#> $has_column_data +#> [1] TRUE +#> +#> $assay_names +#> [1] "counts" "logcounts" +#> +#> $reduced_dimension_names +#> [1] "PCA" "TSNE" +#> list.files(tmp, recursive=TRUE) #> [1] "assays/0/content" "assays/0/stats" #> [3] "assays/0/summary.json" "assays/1/content" @@ -179,6 +213,7 @@

Examples

#> [11] "reduced_dimensions/1/content" "reduced_dimensions/1/summary.json" #> [13] "row_data/content" "row_data/summary.json" #> [15] "summary.json" +