diff --git a/articles/tidyCoverage.html b/articles/tidyCoverage.html index f4369cf..afa4588 100644 --- a/articles/tidyCoverage.html +++ b/articles/tidyCoverage.html @@ -67,7 +67,7 @@

Introduction to tidyCoverage

-

11 December 2023

+

12 December 2023

Source: vignettes/tidyCoverage.Rmd
tidyCoverage.Rmd
@@ -320,21 +320,21 @@

Bin a CoverageExperiment o

Expand a CoverageExperiment object 

-expand(CE)
-#> # A tibble: 5,355,000 × 7
+expand(CE)
+#> # A tibble: 5,355,000 × 8
 #> # Groups:   track, features, ranges [1,785]
-#>    track features chr   ranges         strand coord coverage
-#>    <chr> <chr>    <chr> <chr>          <chr>  <dbl>    <dbl>
-#>  1 track features II    II:4290-7289:+ +       4290        0
-#>  2 track features II    II:4290-7289:+ +       4291        0
-#>  3 track features II    II:4290-7289:+ +       4292        0
-#>  4 track features II    II:4290-7289:+ +       4293        0
-#>  5 track features II    II:4290-7289:+ +       4294        0
-#>  6 track features II    II:4290-7289:+ +       4295        0
-#>  7 track features II    II:4290-7289:+ +       4296        0
-#>  8 track features II    II:4290-7289:+ +       4297        0
-#>  9 track features II    II:4290-7289:+ +       4298        0
-#> 10 track features II    II:4290-7289:+ +       4299        0
+#>    track features chr   ranges         strand coord coverage coord.scaled
+#>    <chr> <chr>    <chr> <chr>          <chr>  <dbl>    <dbl>        <dbl>
+#>  1 track features II    II:4290-7289:+ +       4290        0        -1500
+#>  2 track features II    II:4290-7289:+ +       4291        0        -1499
+#>  3 track features II    II:4290-7289:+ +       4292        0        -1498
+#>  4 track features II    II:4290-7289:+ +       4293        0        -1497
+#>  5 track features II    II:4290-7289:+ +       4294        0        -1496
+#>  6 track features II    II:4290-7289:+ +       4295        0        -1495
+#>  7 track features II    II:4290-7289:+ +       4296        0        -1494
+#>  8 track features II    II:4290-7289:+ +       4297        0        -1493
+#>  9 track features II    II:4290-7289:+ +       4298        0        -1492
+#> 10 track features II    II:4290-7289:+ +       4299        0        -1491
 #> # ℹ 5,354,990 more rows
@@ -352,21 +352,20 @@

Plot cover MNase = system.file("extdata", "MNase.bw", package = "tidyCoverage") ) |> BigWigFileList() -locus <- "II:450001-475000" -CE2 <- CoverageExperiment( +locus <- GRanges("II:450001-475000") +p <- CoverageExperiment( tracks = tracks, - features = GRanges(locus), - width = width (GRanges(locus)) -) |> coarsen(window = width(GRanges(locus))/1000) -CE2 |> - expand() |> + features = locus, + width = width(locus) +) |> + coarsen(window = 25) |> + expand() |> ggplot(aes(x = coord, y = coverage)) + geom_col(aes(fill = track, col = track)) + facet_grid(track~., scales = 'free') + scale_x_continuous(expand = c(0, 0)) + theme_bw() + theme(legend.position = "none", aspect.ratio = 0.1)

-

@@ -687,7 +686,7 @@

Session info#> [8] base #> #> other attached packages: -#> [1] AnnotationHub_3.11.0 BiocFileCache_2.11.1 +#> [1] AnnotationHub_3.11.1 BiocFileCache_2.11.1 #> [3] dbplyr_2.4.0 tidyr_1.3.0 #> [5] dplyr_1.1.4 tidySummarizedExperiment_1.13.0 #> [7] ttservice_0.4.0 plyranges_1.23.0 @@ -697,114 +696,107 @@

Session info#> [15] GenomicRanges_1.55.1 GenomeInfoDb_1.39.1 #> [17] IRanges_2.37.0 S4Vectors_0.41.2 #> [19] BiocGenerics_0.49.1 MatrixGenerics_1.15.0 -#> [21] matrixStats_1.1.0 BiocStyle_2.31.0 +#> [21] matrixStats_1.2.0 BiocStyle_2.31.0 #> #> loaded via a namespace (and not attached): -#> [1] jsonlite_1.8.8 -#> [2] magrittr_2.0.3 -#> [3] GenomicFeatures_1.55.1 -#> [4] farver_2.1.1 -#> [5] rmarkdown_2.25 -#> [6] fs_1.6.3 -#> [7] BiocIO_1.13.0 -#> [8] zlibbioc_1.49.0 -#> [9] ragg_1.2.6 -#> [10] vctrs_0.6.5 -#> [11] memoise_2.0.1 -#> [12] Rsamtools_2.19.2 -#> [13] RCurl_1.98-1.13 -#> [14] htmltools_0.5.7 -#> [15] S4Arrays_1.3.1 -#> [16] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 -#> [17] progress_1.2.3 -#> [18] curl_5.2.0 -#> [19] SparseArray_1.3.1 -#> [20] sass_0.4.8 -#> [21] bslib_0.6.1 -#> [22] htmlwidgets_1.6.4 -#> [23] desc_1.4.3 -#> [24] plotly_4.10.3 -#> [25] cachem_1.0.8 -#> [26] GenomicAlignments_1.39.0 -#> [27] mime_0.12 -#> [28] lifecycle_1.0.4 -#> [29] pkgconfig_2.0.3 -#> [30] Matrix_1.6-4 -#> [31] R6_2.5.1 -#> [32] fastmap_1.1.1 -#> [33] GenomeInfoDbData_1.2.11 -#> [34] shiny_1.8.0 -#> [35] digest_0.6.33 -#> [36] colorspace_2.1-0 -#> [37] AnnotationDbi_1.65.2 -#> [38] textshaping_0.3.7 -#> [39] RSQLite_2.3.4 -#> [40] filelock_1.0.3 -#> [41] labeling_0.4.3 -#> [42] fansi_1.0.6 -#> [43] httr_1.4.7 -#> [44] abind_1.4-5 -#> [45] compiler_4.4.0 -#> [46] bit64_4.0.5 -#> [47] withr_2.5.2 -#> [48] BiocParallel_1.37.0 -#> [49] DBI_1.1.3 -#> [50] highr_0.10 -#> [51] biomaRt_2.59.0 -#> [52] rappdirs_0.3.3 -#> [53] DelayedArray_0.29.0 -#> [54] rjson_0.2.21 -#> [55] tools_4.4.0 -#> [56] interactiveDisplayBase_1.41.0 -#> [57] httpuv_1.6.13 -#> [58] glue_1.6.2 -#> [59] restfulr_0.0.15 -#> [60] promises_1.2.1 -#> [61] grid_4.4.0 -#> [62] generics_0.1.3 -#> [63] gtable_0.3.4 -#> [64] data.table_1.14.10 -#> [65] hms_1.1.3 -#> [66] xml2_1.3.6 -#> [67] utf8_1.2.4 -#> [68] XVector_0.43.0 -#> [69] BiocVersion_3.19.1 -#> [70] pillar_1.9.0 -#> [71] stringr_1.5.1 -#> [72] later_1.3.2 -#> [73] lattice_0.22-5 -#> [74] bit_4.0.5 -#> [75] tidyselect_1.2.0 -#> [76] Biostrings_2.71.1 -#> [77] knitr_1.45 -#> [78] bookdown_0.37 -#> [79] xfun_0.41 -#> [80] stringi_1.8.2 -#> [81] lazyeval_0.2.2 -#> [82] yaml_2.3.8 -#> [83] evaluate_0.23 -#> [84] codetools_0.2-19 -#> [85] tibble_3.2.1 -#> [86] BiocManager_1.30.22 -#> [87] cli_3.6.2 -#> [88] xtable_1.8-4 -#> [89] systemfonts_1.0.5 -#> [90] munsell_0.5.0 -#> [91] jquerylib_0.1.4 -#> [92] Rcpp_1.0.11 -#> [93] png_0.1-8 -#> [94] XML_3.99-0.16 -#> [95] parallel_4.4.0 -#> [96] ellipsis_0.3.2 -#> [97] pkgdown_2.0.7 -#> [98] blob_1.2.4 -#> [99] prettyunits_1.2.0 -#> [100] bitops_1.0-7 -#> [101] viridisLite_0.4.2 -#> [102] scales_1.3.0 -#> [103] crayon_1.5.2 -#> [104] rlang_1.1.2 -#> [105] KEGGREST_1.43.0

+#> [1] DBI_1.1.3 +#> [2] bitops_1.0-7 +#> [3] biomaRt_2.59.0 +#> [4] rlang_1.1.2 +#> [5] magrittr_2.0.3 +#> [6] compiler_4.4.0 +#> [7] RSQLite_2.3.4 +#> [8] GenomicFeatures_1.55.1 +#> [9] png_0.1-8 +#> [10] systemfonts_1.0.5 +#> [11] vctrs_0.6.5 +#> [12] stringr_1.5.1 +#> [13] pkgconfig_2.0.3 +#> [14] crayon_1.5.2 +#> [15] fastmap_1.1.1 +#> [16] XVector_0.43.0 +#> [17] ellipsis_0.3.2 +#> [18] labeling_0.4.3 +#> [19] utf8_1.2.4 +#> [20] Rsamtools_2.19.2 +#> [21] rmarkdown_2.25 +#> [22] ragg_1.2.6 +#> [23] bit_4.0.5 +#> [24] xfun_0.41 +#> [25] zlibbioc_1.49.0 +#> [26] cachem_1.0.8 +#> [27] jsonlite_1.8.8 +#> [28] progress_1.2.3 +#> [29] blob_1.2.4 +#> [30] highr_0.10 +#> [31] DelayedArray_0.29.0 +#> [32] BiocParallel_1.37.0 +#> [33] prettyunits_1.2.0 +#> [34] parallel_4.4.0 +#> [35] R6_2.5.1 +#> [36] bslib_0.6.1 +#> [37] stringi_1.8.3 +#> [38] jquerylib_0.1.4 +#> [39] bookdown_0.37 +#> [40] knitr_1.45 +#> [41] Matrix_1.6-4 +#> [42] tidyselect_1.2.0 +#> [43] abind_1.4-5 +#> [44] yaml_2.3.8 +#> [45] codetools_0.2-19 +#> [46] curl_5.2.0 +#> [47] lattice_0.22-5 +#> [48] tibble_3.2.1 +#> [49] withr_2.5.2 +#> [50] KEGGREST_1.43.0 +#> [51] evaluate_0.23 +#> [52] desc_1.4.3 +#> [53] xml2_1.3.6 +#> [54] Biostrings_2.71.1 +#> [55] filelock_1.0.3 +#> [56] pillar_1.9.0 +#> [57] BiocManager_1.30.22 +#> [58] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 +#> [59] plotly_4.10.3 +#> [60] generics_0.1.3 +#> [61] RCurl_1.98-1.13 +#> [62] BiocVersion_3.19.1 +#> [63] hms_1.1.3 +#> [64] munsell_0.5.0 +#> [65] scales_1.3.0 +#> [66] glue_1.6.2 +#> [67] lazyeval_0.2.2 +#> [68] tools_4.4.0 +#> [69] BiocIO_1.13.0 +#> [70] data.table_1.14.10 +#> [71] GenomicAlignments_1.39.0 +#> [72] fs_1.6.3 +#> [73] XML_3.99-0.16 +#> [74] grid_4.4.0 +#> [75] AnnotationDbi_1.65.2 +#> [76] colorspace_2.1-0 +#> [77] GenomeInfoDbData_1.2.11 +#> [78] restfulr_0.0.15 +#> [79] cli_3.6.2 +#> [80] rappdirs_0.3.3 +#> [81] textshaping_0.3.7 +#> [82] fansi_1.0.6 +#> [83] S4Arrays_1.3.1 +#> [84] viridisLite_0.4.2 +#> [85] gtable_0.3.4 +#> [86] sass_0.4.8 +#> [87] digest_0.6.33 +#> [88] SparseArray_1.3.1 +#> [89] rjson_0.2.21 +#> [90] htmlwidgets_1.6.4 +#> [91] farver_2.1.1 +#> [92] memoise_2.0.1 +#> [93] htmltools_0.5.7 +#> [94] pkgdown_2.0.7 +#> [95] lifecycle_1.0.4 +#> [96] httr_1.4.7 +#> [97] mime_0.12 +#> [98] bit64_4.0.5
diff --git a/index.html b/index.html index 9cae2de..db775ef 100644 --- a/index.html +++ b/index.html @@ -123,7 +123,7 @@

Plot coverage over a single locus 
 CoverageExperiment(tracks, GRanges("II:450001-455000"), width = 5000) |> 
-    expand() |> 
+    expand() |> 
     ggplot(aes(x = coord, y = coverage)) + 
         geom_col(aes(fill = track, col = track)) + 
         facet_grid(track~., scales = 'free') + 
diff --git a/pkgdown.yml b/pkgdown.yml
index 285ae84..546ec63 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,5 +3,5 @@ pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
   tidyCoverage: tidyCoverage.html
-last_built: 2023-12-11T22:51Z
+last_built: 2023-12-12T20:38Z
 
diff --git a/reference/expand.html b/reference/expand.html
index 75a072b..0e2cda8 100644
--- a/reference/expand.html
+++ b/reference/expand.html
@@ -66,17 +66,17 @@
 
     

     
Usage

-    
# S4 method for CoverageExperiment
-expand(x, ...)

+    
# S3 method for CoverageExperiment
+expand(data, ..., .name_repair = NULL)

     

 
     

     
Arguments

-    
x

+    
data

 
a CoverageExperiment object

 
 
-
...

+
..., .name_repair

 
ignored

 
 

@@ -101,21 +101,21 @@ 
Examples#> colData names(1): track
 #> width: 3000
 
-expand(ce)
-#> # A tibble: 368,400 × 7
+expand(ce)
+#> # A tibble: 368,400 × 8
 #> # Groups:   track, features, ranges [1,228]
-#>    track   features chr   ranges         strand coord coverage
-#>    <chr>   <chr>    <chr> <chr>          <chr>  <dbl>    <dbl>
-#>  1 RNA_fwd Scc1     II    II:4290-7289:+ +       4290   -0.257
-#>  2 RNA_fwd Scc1     II    II:4290-7289:+ +       4300   -0.257
-#>  3 RNA_fwd Scc1     II    II:4290-7289:+ +       4310   -0.257
-#>  4 RNA_fwd Scc1     II    II:4290-7289:+ +       4320   -0.257
-#>  5 RNA_fwd Scc1     II    II:4290-7289:+ +       4330   -0.257
-#>  6 RNA_fwd Scc1     II    II:4290-7289:+ +       4340   -0.257
-#>  7 RNA_fwd Scc1     II    II:4290-7289:+ +       4350   -0.257
-#>  8 RNA_fwd Scc1     II    II:4290-7289:+ +       4360   -0.257
-#>  9 RNA_fwd Scc1     II    II:4290-7289:+ +       4370   -0.257
-#> 10 RNA_fwd Scc1     II    II:4290-7289:+ +       4380   -0.257
+#>    track   features chr   ranges         strand coord coverage coord.scaled
+#>    <chr>   <chr>    <chr> <chr>          <chr>  <dbl>    <dbl>        <dbl>
+#>  1 RNA_fwd Scc1     II    II:4290-7289:+ +       4290   -0.257        -1500
+#>  2 RNA_fwd Scc1     II    II:4290-7289:+ +       4300   -0.257        -1490
+#>  3 RNA_fwd Scc1     II    II:4290-7289:+ +       4310   -0.257        -1480
+#>  4 RNA_fwd Scc1     II    II:4290-7289:+ +       4320   -0.257        -1470
+#>  5 RNA_fwd Scc1     II    II:4290-7289:+ +       4330   -0.257        -1460
+#>  6 RNA_fwd Scc1     II    II:4290-7289:+ +       4340   -0.257        -1450
+#>  7 RNA_fwd Scc1     II    II:4290-7289:+ +       4350   -0.257        -1440
+#>  8 RNA_fwd Scc1     II    II:4290-7289:+ +       4360   -0.257        -1430
+#>  9 RNA_fwd Scc1     II    II:4290-7289:+ +       4370   -0.257        -1420
+#> 10 RNA_fwd Scc1     II    II:4290-7289:+ +       4380   -0.257        -1410
 #> # ℹ 368,390 more rows
diff --git a/reference/reexports.html b/reference/reexports.html index e24686c..a864c86 100644 --- a/reference/reexports.html +++ b/reference/reexports.html @@ -7,7 +7,11 @@ S4Vectors -aggregate, expand +aggregate + + + tidyr +expand ">Objects exported from other packages — reexports • tidyCoverage