Basic documentation updates for introspection of a store (#76)

vignettes/basics.Rmd

@@ -7,49 +7,48 @@ vignette: >
   %\VignetteEncoding{UTF-8}
 ---
 
+```{r, include = FALSE}
+  knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>",
+  out.width = "100%"
+)
+```
+
 ## Load the package
 
-```r
+```{r}
 library(pizzarr)
 ```
 
 ## Create an empty ZarrArray
 
-```r
+```{r}
+(a <- array(data=1:20, dim=c(2, 10)))
+
 z <- zarr_create_empty(shape=dim(a), dtype="<f4")
 ```
 
 ## Create a ZarrArray based on a base R array
 
-```r
-a <- array(data=1:20, dim=c(2, 10))
-#      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
-# [1,]    1    3    5    7    9   11   13   15   17    19
-# [2,]    2    4    6    8   10   12   14   16   18    20
+```{r}
 z <- zarr_create_array(data = a, shape=dim(a), dtype="<f4", fill_value=NA)
 
 # R-like one-based slicing
 s1 <- z$get_item(list(slice(1, 2), slice(1, 5)))
 
 print(s1$data)
-#      [,1] [,2] [,3] [,4] [,5]
-# [1,]    1    3    5    7    9
-# [2,]    2    4    6    8   10
-
 
 # Python-like zero-based slicing
 s2 <- z$get_item(list(zb_slice(0, 2), zb_slice(0, 5)))
 
 print(s2$data)
-# Imagine the printed indices as:
-#      [,0] [,1] [,2] [,3] [,4]
-# [0,]    1    3    5    7    9
-# [1,]    2    4    6    8   10
+
 ```
 
 ## Create nested ZarrGroups and ZarrArrays
 
-```r
+```{r}
 g1 <- zarr_create_group()
 g2 <- g1$create_group("foo")
 g3 <- g2$create_group("bar")
@@ -58,33 +57,69 @@ data <- array(data=1:10, dim=c(2, 5))
 a <- g3$create_dataset("baz", data=data, shape=dim(data))
 
 print(a$get_name())
-# [1] "/foo/bar/baz"
 
 print(a$get_shape())
-# [1] 2 5
+```
+
+## List arrays in a zarr root group
+
+```{r}
+root <- system.file("extdata", "fixtures", "v2", "data.zarr", package="pizzarr")
+
+z <- zarr_open(root)
+
+class(z)
+
+store <- z$get_store()
+
+class(store)
+
+print(store$listdir())
 ```
 
 ## Open a ZarrArray from a DirectoryStore (convenience)
 
-```r
+```{r}
 root <- system.file("extdata", "fixtures", "v2", "data.zarr", package="pizzarr")
 
 g <- zarr_open_group(root)
 a <- g$get_item("1d.contiguous.lz4.i2")
 
 print(a$get_shape())
-# [1] 4
 ```
 
 ## Open a ZarrArray from a DirectoryStore
 
-```r
+```{r}
 root <- system.file("extdata", "fixtures", "v2", "data.zarr", package="pizzarr")
     
 store <- DirectoryStore$new(root)
 g <- ZarrGroup$new(store)
 a <- g$get_item("1d.contiguous.lz4.i2")
 
 print(a$get_shape())
-# [1] 4
+```
+
+## Get attributes from a root group and ZarrArray
+
+```{r}
+root <- system.file("extdata", "dog.ome.zarr", package="pizzarr")
+
+z <- zarr_open(root)
+
+class(z)
+
+attrs <- z$get_attrs()$to_list()
+
+names(attrs)
+
+lengths(attrs$omero)
+
+z$get_store()$listdir()
+
+a <- z$get_item("4")
+
+class(a)
+
+a$get_attrs()$to_list()
 ```