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  1. tidyCoverage
  2. NAMESPACE
Browse code

feat: more geoms

Jacques authored on 12/07/2024 20:56:30
Showing 1 changed files
NAMESPACE
History View file @ f85d4dc
... ... 
@@ -12,6 +12,9 @@ export(as_tibble)
12 12 
 export(coarsen)
13 13 
 export(expand)
14 14 
 export(geom_aggrcoverage)
15 
+export(geom_coverage)
16 
+export(scale_x_genome)
17 
+export(scale_y_coverage)
15 18 
 export(show)
16 19 
 exportMethods(CoverageExperiment)
17 20 
 exportMethods(aggregate)
... ... 
@@ -45,6 +48,8 @@ importFrom(purrr,map_chr)
45 48 
 importFrom(rlang,names2)
46 49 
 importFrom(rtracklayer,BigWigFile)
47 50 
 importFrom(rtracklayer,BigWigFileList)
51 
+importFrom(scales,oob_squish)
52 
+importFrom(scales,unit_format)
48 53 
 importFrom(stats,qt)
49 54 
 importFrom(stats,setNames)
50 55 
 importFrom(tidyr,all_of)
Browse code

feat: geom_aggrcoverage

js2264 authored on 11/07/2024 19:47:26
Showing 1 changed files
NAMESPACE
History View file @ d0c89d4
... ... 
@@ -11,6 +11,7 @@ export(aggregate)
11 11 
 export(as_tibble)
12 12 
 export(coarsen)
13 13 
 export(expand)
14 
+export(geom_aggrcoverage)
14 15 
 export(show)
15 16 
 exportMethods(CoverageExperiment)
16 17 
 exportMethods(aggregate)
... ... 
@@ -19,6 +20,7 @@ exportMethods(show)
19 20 
 import(GenomeInfoDb)
20 21 
 import(GenomicRanges)
21 22 
 import(SummarizedExperiment)
23 
+import(ggplot2)
22 24 
 import(methods)
23 25 
 importFrom(BiocIO,resource)
24 26 
 importFrom(BiocParallel,bplapply)
Browse code

fix: add an expand method from tidyr generic rather than S4Vectors

js2264 authored on 12/12/2023 19:50:28
Showing 1 changed files
NAMESPACE
History View file @ a4322ad
... ... 
@@ -1,6 +1,7 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 3 
 S3method(as_tibble,AggregatedCoverage)
4 
+S3method(expand,CoverageExperiment)
4 5 
 S3method(print,AggregatedCoverage)
5 6 
 S3method(print,CoverageExperiment)
6 7 
 S3method(tbl_format_header,tidyAggregatedCoverage)
... ... 
@@ -14,7 +15,6 @@ export(show)
14 15 
 exportMethods(CoverageExperiment)
15 16 
 exportMethods(aggregate)
16 17 
 exportMethods(coarsen)
17 
-exportMethods(expand)
18 18 
 exportMethods(show)
19 19 
 import(GenomeInfoDb)
20 20 
 import(GenomicRanges)
... ... 
@@ -25,7 +25,6 @@ importFrom(BiocParallel,bplapply)
25 25 
 importFrom(BiocParallel,bpparam)
26 26 
 importFrom(IRanges,NumericList)
27 27 
 importFrom(S4Vectors,aggregate)
28 
-importFrom(S4Vectors,expand)
29 28 
 importFrom(SummarizedExperiment,assayNames)
30 29 
 importFrom(cli,console_width)
31 30 
 importFrom(cli,symbol)
... ... 
@@ -48,5 +47,6 @@ importFrom(stats,qt)
48 47 
 importFrom(stats,setNames)
49 48 
 importFrom(tidyr,all_of)
50 49 
 importFrom(tidyr,any_of)
50 
+importFrom(tidyr,expand)
51 51 
 importFrom(tidyr,pivot_longer)
52 52 
 importFrom(vctrs,new_data_frame)
Browse code

fix: NAMESPACE

js2264 authored on 11/12/2023 22:07:55
Showing 1 changed files
NAMESPACE
History View file @ 7fcd589
... ... 
@@ -20,6 +20,7 @@ import(GenomeInfoDb)
20 20 
 import(GenomicRanges)
21 21 
 import(SummarizedExperiment)
22 22 
 import(methods)
23 
+importFrom(BiocIO,resource)
23 24 
 importFrom(BiocParallel,bplapply)
24 25 
 importFrom(BiocParallel,bpparam)
25 26 
 importFrom(IRanges,NumericList)
Browse code

fix: reduce bundle size

js2264 authored on 11/12/2023 21:46:50
Showing 1 changed files
NAMESPACE
History View file @ 669daf0
... ... 
@@ -9,6 +9,7 @@ export(CoverageExperiment)
9 9 
 export(aggregate)
10 10 
 export(as_tibble)
11 11 
 export(coarsen)
12 
+export(expand)
12 13 
 export(show)
13 14 
 exportMethods(CoverageExperiment)
14 15 
 exportMethods(aggregate)
Browse code

feat: add expand method for CoverageExperiment

js2264 authored on 05/12/2023 15:20:14
Showing 1 changed files
NAMESPACE
History View file @ 3139dd5
... ... 
@@ -13,6 +13,7 @@ export(show)
13 13 
 exportMethods(CoverageExperiment)
14 14 
 exportMethods(aggregate)
15 15 
 exportMethods(coarsen)
16 
+exportMethods(expand)
16 17 
 exportMethods(show)
17 18 
 import(GenomeInfoDb)
18 19 
 import(GenomicRanges)
... ... 
@@ -22,6 +23,7 @@ importFrom(BiocParallel,bplapply)
22 23 
 importFrom(BiocParallel,bpparam)
23 24 
 importFrom(IRanges,NumericList)
24 25 
 importFrom(S4Vectors,aggregate)
26 
+importFrom(S4Vectors,expand)
25 27 
 importFrom(SummarizedExperiment,assayNames)
26 28 
 importFrom(cli,console_width)
27 29 
 importFrom(cli,symbol)
Browse code

fix: print for CoverageExperiment objects

js2264 authored on 05/12/2023 14:30:42
Showing 1 changed files
NAMESPACE
History View file @ 71c93d0
... ... 
@@ -2,7 +2,9 @@
2 2
3 3 
 S3method(as_tibble,AggregatedCoverage)
4 4 
 S3method(print,AggregatedCoverage)
5 
+S3method(print,CoverageExperiment)
5 6 
 S3method(tbl_format_header,tidyAggregatedCoverage)
7 
+S3method(tbl_format_header,tidyCoverageExperiment)
6 8 
 export(CoverageExperiment)
7 9 
 export(aggregate)
8 10 
 export(as_tibble)
Browse code

temp fix: rm as_tibble method for CE objects

js2264 authored on 05/12/2023 08:59:52
Showing 1 changed files
NAMESPACE
History View file @ 324006c
... ... 
@@ -1,7 +1,6 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 3 
 S3method(as_tibble,AggregatedCoverage)
4 
-S3method(as_tibble,CoverageExperiment)
5 4 
 S3method(print,AggregatedCoverage)
6 5 
 S3method(tbl_format_header,tidyAggregatedCoverage)
7 6 
 export(CoverageExperiment)
Browse code

doc: update

js2264 authored on 27/11/2023 11:38:54
Showing 1 changed files
NAMESPACE
History View file @ 031b5af
... ... 
@@ -41,4 +41,7 @@ importFrom(rtracklayer,BigWigFile)
41 41 
 importFrom(rtracklayer,BigWigFileList)
42 42 
 importFrom(stats,qt)
43 43 
 importFrom(stats,setNames)
44 
+importFrom(tidyr,all_of)
45 
+importFrom(tidyr,any_of)
46 
+importFrom(tidyr,pivot_longer)
44 47 
 importFrom(vctrs,new_data_frame)
Browse code

feat: as_tibble for CoverageExperiment as well

js2264 authored on 27/11/2023 10:40:16
Showing 1 changed files
NAMESPACE
History View file @ 2ba8a4f
... ... 
@@ -1,6 +1,7 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 3 
 S3method(as_tibble,AggregatedCoverage)
4 
+S3method(as_tibble,CoverageExperiment)
4 5 
 S3method(print,AggregatedCoverage)
5 6 
 S3method(tbl_format_header,tidyAggregatedCoverage)
6 7 
 export(CoverageExperiment)
Browse code

feaet: coarsen CoverageExperiment

js2264 authored on 27/11/2023 08:05:27
Showing 1 changed files
NAMESPACE
History View file @ 5aa65e5
... ... 
@@ -6,9 +6,11 @@ S3method(tbl_format_header,tidyAggregatedCoverage)
6 6 
 export(CoverageExperiment)
7 7 
 export(aggregate)
8 8 
 export(as_tibble)
9 
+export(coarsen)
9 10 
 export(show)
10 11 
 exportMethods(CoverageExperiment)
11 12 
 exportMethods(aggregate)
13 
+exportMethods(coarsen)
12 14 
 exportMethods(show)
13 15 
 import(GenomeInfoDb)
14 16 
 import(GenomicRanges)
Browse code

feat: can flip coverage according to strandness

js2264 authored on 26/11/2023 00:21:53
Showing 1 changed files
NAMESPACE
History View file @ 957d8fb
... ... 
@@ -34,6 +34,8 @@ importFrom(pillar,style_subtle)
34 34 
 importFrom(pillar,tbl_format_header)
35 35 
 importFrom(purrr,map_chr)
36 36 
 importFrom(rlang,names2)
37 
+importFrom(rtracklayer,BigWigFile)
38 
+importFrom(rtracklayer,BigWigFileList)
37 39 
 importFrom(stats,qt)
38 40 
 importFrom(stats,setNames)
39 41 
 importFrom(vctrs,new_data_frame)
Browse code

feat: define CoverageExperiment and AggregatedCoverage classes and aggregate methods

js2264 authored on 25/11/2023 23:50:46
Showing 1 changed files
NAMESPACE
History View file @ 1951d87
... ... 
@@ -1,11 +1,12 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 
-S3method(as_tibble,CoverageExperiment)
4 
-S3method(print,CoverageExperiment)
5 
-S3method(tbl_format_header,tidyCoverageExperiment)
3 
+S3method(as_tibble,AggregatedCoverage)
4 
+S3method(print,AggregatedCoverage)
5 
+S3method(tbl_format_header,tidyAggregatedCoverage)
6 6 
 export(CoverageExperiment)
7 7 
 export(aggregate)
8 8 
 export(as_tibble)
9 
+export(show)
9 10 
 exportMethods(CoverageExperiment)
10 11 
 exportMethods(aggregate)
11 12 
 exportMethods(show)
Browse code

first push

js2264 authored on 25/11/2023 08:25:58
Showing 1 changed files
NAMESPACE
History View file @ 4a79c07
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,38 @@
1 
+# Generated by roxygen2: do not edit by hand
2 
+
3 
+S3method(as_tibble,CoverageExperiment)
4 
+S3method(print,CoverageExperiment)
5 
+S3method(tbl_format_header,tidyCoverageExperiment)
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+export(CoverageExperiment)
7 
+export(aggregate)
8 
+export(as_tibble)
9 
+exportMethods(CoverageExperiment)
10 
+exportMethods(aggregate)
11 
+exportMethods(show)
12 
+import(GenomeInfoDb)
13 
+import(GenomicRanges)
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+import(SummarizedExperiment)
15 
+import(methods)
16 
+importFrom(BiocParallel,bplapply)
17 
+importFrom(BiocParallel,bpparam)
18 
+importFrom(IRanges,NumericList)
19 
+importFrom(S4Vectors,aggregate)
20 
+importFrom(SummarizedExperiment,assayNames)
21 
+importFrom(cli,console_width)
22 
+importFrom(cli,symbol)
23 
+importFrom(dplyr,as_tibble)
24 
+importFrom(dplyr,bind_cols)
25 
+importFrom(dplyr,bind_rows)
26 
+importFrom(dplyr,filter)
27 
+importFrom(dplyr,mutate)
28 
+importFrom(dplyr,relocate)
29 
+importFrom(fansi,strwrap_ctl)
30 
+importFrom(pillar,align)
31 
+importFrom(pillar,get_extent)
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+importFrom(pillar,style_subtle)
33 
+importFrom(pillar,tbl_format_header)
34 
+importFrom(purrr,map_chr)
35 
+importFrom(rlang,names2)
36 
+importFrom(stats,qt)
37 
+importFrom(stats,setNames)
38 
+importFrom(vctrs,new_data_frame)