@@ -119,8 +123,9 @@
+Basics: importin #> Attaching package: 'rtracklayer' #> The following object is masked from 'package:AnnotationHub': #> -#> hubUrl -library(InteractionSet) +#> hubUrl
+library(InteractionSet)
#> Loading required package: SummarizedExperiment
#> Loading required package: MatrixGenerics
#> Loading required package: matrixStats
@@ -167,15 +172,17 @@ Basics: importin
#> cache
#> The following object is masked from 'package:AnnotationHub':
#>
-#> cache
-cool_file <- HiContactsData('yeast_wt', format = 'cool')
+#> cache
+cool_file <- HiContactsData('yeast_wt', format = 'cool')
#> see ?HiContactsData and browseVignettes('HiContactsData') for documentation
-#> loading from cache
-hic <- import(cool_file, format = 'cool')
+#> loading from cache+hic <- import(cool_file, format = 'cool') hic #> `HiCExperiment` object with 8,757,906 contacts over 12,079 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/8ee93e8ac2_7751" +#> fileName: "/github/home/.cache/R/ExperimentHub/11545042987d_7751" #> focus: "whole genome" #> resolutions(1): 1000 #> active resolution: 1000 @@ -199,11 +206,11 @@simply takes the first scores available. -Plot matrix heatmapsplotMatrix()
diff --git a/reference/palettes.html b/reference/palettes.html index f03e81e..7972370 100644 --- a/reference/palettes.html +++ b/reference/palettes.html @@ -1,5 +1,5 @@ -+## Square matrix plotMatrix(hic, use.scores = 'balanced', limits = c(-4, -1))-
@@ -131,7 +131,7 @@+diff --git a/reference/getLoops.html b/reference/getLoops.html index e6ea988..c9419ab 100644 --- a/reference/getLoops.html +++ b/reference/getLoops.html @@ -1,5 +1,5 @@ -## Horizontal matrix plotMatrix( @@ -224,11 +231,12 @@function. -Plot loopsInteractionSet::makeGInteractionsFromGRangesPairs()
++mcool_file <- HiContactsData('yeast_wt', format = 'mcool') #> see ?HiContactsData and browseVignettes('HiContactsData') for documentation -#> loading from cache -loops <- system.file("extdata", 'S288C-loops.bedpe', package = 'HiCExperiment') |> +#> loading from cache@@ -109,7 +109,7 @@+loops <- system.file("extdata", 'S288C-loops.bedpe', package = 'HiCExperiment') |> import() |> makeGInteractionsFromGRangesPairs() p <- import(mcool_file, format = 'mcool', focus = 'IV') |> @@ -237,7 +245,7 @@Plot loops
Plot borders
-diff --git a/reference/getCompartments.html b/reference/getCompartments.html index 6df7b22..1264ab0 100644 --- a/reference/getCompartments.html +++ b/reference/getCompartments.html @@ -1,5 +1,5 @@ -+borders <- system.file("extdata", 'S288C-borders.bed', package = 'HiCExperiment') |> import() p <- import(mcool_file, format = 'mcool', focus = 'IV') |> @@ -246,15 +254,16 @@Plot borders
Plot aggregated matrices over features
-++aggr_centros <- HiContacts::aggregate( hic, targets = loops, BPPARAM = BiocParallel::SerialParam() ) #> Going through preflight checklist... #> Parsing the entire contact matrice as a sparse matrix... #> Modeling distance decay... -#> Filtering for contacts within provided targets... -plotMatrix( +#> Filtering for contacts within provided targets...@@ -267,26 +276,30 @@+plotMatrix( aggr_centros, use.scores = 'detrended', limits = c(-1, 1), scale = 'linear', cmap = bgrColors() )Arithmetics
Computing autocorrelated contact map
-+++mcool_file <- HiContactsData('mESCs', format = 'mcool') #> see ?HiContactsData and browseVignettes('HiContactsData') for documentation -#> loading from cache -hic <- import(mcool_file, format = 'mcool', focus = 'chr2', resolution = 160000) +#> loading from cache++hic <- import(mcool_file, format = 'mcool', focus = 'chr2', resolution = 160000) hic <- autocorrelate(hic) -#> -scores(hic) +#>++scores(hic) #> List of length 5 -#> names(5): count balanced expected detrended autocorrelated -summary(scores(hic, 'autocorrelated')) +#> names(5): count balanced expected detrended autocorrelated+#> -0.499 -0.097 0.040 0.043 0.172 1.000 7739+summary(scores(hic, 'autocorrelated')) #> Min. 1st Qu. Median Mean 3rd Qu. Max. NA's -#> -0.499 -0.097 0.040 0.043 0.172 1.000 7739 -plotMatrix(hic, use.scores = 'autocorrelated', limits = c(-1, 1), scale = 'linear')+plotMatrix(hic, use.scores = 'autocorrelated', limits = c(-1, 1), scale = 'linear')
@@ -110,7 +110,7 @@Detrending contact map (map of scores over expected)
-diff --git a/reference/checks.html b/reference/checks.html index 8900257..d9e08a6 100644 --- a/reference/checks.html +++ b/reference/checks.html @@ -1,5 +1,5 @@ -+hic <- import(mcool_file, format = 'mcool', focus = 'chr18:20000000-35000000', resolution = 40000) detrended_hic <- detrend(hic) patchwork::wrap_plots( @@ -298,20 +311,22 @@Detrending contact m
@@ -234,7 +234,7 @@Summing two maps
-diff --git a/reference/Ps.html b/reference/Ps.html index e8555b8..4ef05f0 100644 --- a/reference/Ps.html +++ b/reference/Ps.html @@ -1,5 +1,5 @@ -++mcool_file_1 <- HiContactsData('yeast_eco1', format = 'mcool') #> see ?HiContactsData and browseVignettes('HiContactsData') for documentation -#> loading from cache -mcool_file_2 <- HiContactsData('yeast_wt', format = 'mcool') +#> loading from cache++mcool_file_2 <- HiContactsData('yeast_wt', format = 'mcool') #> see ?HiContactsData and browseVignettes('HiContactsData') for documentation -#> loading from cache -hic_1 <- import(mcool_file_1, format = 'mcool', focus = 'II:1-300000', resolution = 2000) +#> loading from cache++hic_1 <- import(mcool_file_1, format = 'mcool', focus = 'II:1-300000', resolution = 2000) hic_2 <- import(mcool_file_2, format = 'mcool', focus = 'II:1-300000', resolution = 2000) merged_hic <- merge(hic_1, hic_2) hic_1 #> `HiCExperiment` object with 301,285 contacts over 150 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/8ee79d66ed6_7754" +#> fileName: "/github/home/.cache/R/ExperimentHub/1154359fc54_7754" #> focus: "II:1-300,000" #> resolutions(5): 1000 2000 4000 8000 16000 #> active resolution: 2000 @@ -319,11 +334,12 @@Summing two maps#> scores(2): count balanced #> topologicalFeatures: compartments(0) borders(0) loops(0) viewpoints(0) #> pairsFile: N/A -#> metadata(0): -hic_2 +#> metadata(0):
++hic_2 #> `HiCExperiment` object with 146,812 contacts over 150 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/8ee50b5962e_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/115453d59c5e_7752" #> focus: "II:1-300,000" #> resolutions(5): 1000 2000 4000 8000 16000 #> active resolution: 2000 @@ -331,11 +347,12 @@Summing two maps#> scores(2): count balanced #> topologicalFeatures: compartments(0) borders(0) loops(0) viewpoints(0) #> pairsFile: N/A -#> metadata(0): -merged_hic +#> metadata(0):
+merged_hic #> `HiCExperiment` object with 229,926 contacts over 150 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/8ee79d66ed6_7754" +#> fileName: "/github/home/.cache/R/ExperimentHub/1154359fc54_7754" #> focus: "II:1-300,000" #> resolutions(5): 1000 2000 4000 8000 16000 #> active resolution: 2000 @@ -348,7 +365,7 @@Summing two maps
Computing ratio between two maps
-@@ -77,7 +77,7 @@++hic_1 <- import(mcool_file_1, format = 'mcool', focus = 'II', resolution = 2000) hic_2 <- import(mcool_file_2, format = 'mcool', focus = 'II', resolution = 2000) div_hic <- divide(hic_1, by = hic_2) @@ -363,8 +380,9 @@Computing ratio between two maps#> scores(6): count.x balanced.x count.by balanced.by balanced.fc balanced.l2fc #> topologicalFeatures: () #> pairsFile: N/A -#> metadata(2): hce_list operation -p <- patchwork::wrap_plots( +#> metadata(2): hce_list operation
diff --git a/index.html b/index.html index 3258b74..9a10bae 100644 --- a/index.html +++ b/index.html @@ -6,14 +6,13 @@+p <- patchwork::wrap_plots( plotMatrix(hic_1, use.scores = 'balanced', scale = 'log10', limits = c(-4, -1)), plotMatrix(hic_2, use.scores = 'balanced', scale = 'log10', limits = c(-4, -1)), plotMatrix(div_hic, use.scores = 'balanced.fc', scale = 'log2', limits = c(-2, 2), cmap = bwrColors()) @@ -373,7 +391,7 @@Computing ratio between two maps
Despeckling (smoothing out) a contact map
-@@ -44,7 +44,7 @@+diff --git a/authors.html b/authors.html index 3db4ac4..54d7f68 100644 --- a/authors.html +++ b/authors.html @@ -1,5 +1,5 @@ -hic_1_despeckled <- despeckle(hic_1) hic_1_despeckled5 <- despeckle(hic_1, focal.size = 5) p <- patchwork::wrap_plots( @@ -389,21 +407,23 @@Mapping topological features
Chromosome compartments
-++mcool_file <- HiContactsData('yeast_wt', format = 'mcool') #> see ?HiContactsData and browseVignettes('HiContactsData') for documentation -#> loading from cache -hic <- import(mcool_file, format = 'mcool', resolution = 16000) +#> loading from cache++hic <- import(mcool_file, format = 'mcool', resolution = 16000) # - Get compartments hic <- getCompartments(hic, chromosomes = c('XV', 'XVI')) #> Going through preflight checklist... #> Parsing intra-chromosomal contacts for each chromosome... -#> Computing eigenvectors for each chromosome... -hic +#> Computing eigenvectors for each chromosome...++hic #> `HiCExperiment` object with 8,757,906 contacts over 763 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/8ee50b5962e_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/115453d59c5e_7752" #> focus: "whole genome" #> resolutions(5): 1000 2000 4000 8000 16000 #> active resolution: 16000 @@ -411,8 +431,9 @@Chromosome compartments#> scores(2): count balanced #> topologicalFeatures: compartments(18) borders(0) loops(0) viewpoints(0) #> pairsFile: N/A -#> metadata(1): eigens - +#> metadata(1): eigens
@@ -62,7 +62,7 @@+# - Export compartments as bigwig and bed files export(IRanges::coverage(metadata(hic)$eigens, weight = 'eigen'), 'compartments.bw') export( @@ -431,7 +452,7 @@Chromosome compartments
Diamond insulation score and chromatin domains borders
-diff --git a/articles/HiContacts_files/figure-html/unnamed-chunk-4-1.png b/articles/HiContacts_files/figure-html/unnamed-chunk-4-1.png index 10f03aa..2f24a18 100644 Binary files a/articles/HiContacts_files/figure-html/unnamed-chunk-4-1.png and b/articles/HiContacts_files/figure-html/unnamed-chunk-4-1.png differ diff --git a/articles/HiContacts_files/figure-html/unnamed-chunk-4-2.png b/articles/HiContacts_files/figure-html/unnamed-chunk-4-2.png index c531135..bcb8180 100644 Binary files a/articles/HiContacts_files/figure-html/unnamed-chunk-4-2.png and b/articles/HiContacts_files/figure-html/unnamed-chunk-4-2.png differ diff --git a/articles/HiContacts_files/figure-html/unnamed-chunk-7-1.png b/articles/HiContacts_files/figure-html/unnamed-chunk-7-1.png index 821c989..2c38143 100644 Binary files a/articles/HiContacts_files/figure-html/unnamed-chunk-7-1.png and b/articles/HiContacts_files/figure-html/unnamed-chunk-7-1.png differ diff --git a/articles/HiContacts_files/figure-html/unnamed-chunk-8-1.png b/articles/HiContacts_files/figure-html/unnamed-chunk-8-1.png index d5e8bec..69fed63 100644 Binary files a/articles/HiContacts_files/figure-html/unnamed-chunk-8-1.png and b/articles/HiContacts_files/figure-html/unnamed-chunk-8-1.png differ diff --git a/articles/HiContacts_files/figure-html/unnamed-chunk-9-1.png b/articles/HiContacts_files/figure-html/unnamed-chunk-9-1.png index c26e32e..f2f01c0 100644 Binary files a/articles/HiContacts_files/figure-html/unnamed-chunk-9-1.png and b/articles/HiContacts_files/figure-html/unnamed-chunk-9-1.png differ diff --git a/articles/index.html b/articles/index.html index 84e2f2f..4c31907 100644 --- a/articles/index.html +++ b/articles/index.html @@ -1,5 +1,5 @@ -++# - Compute insulation score hic <- refocus(hic, 'II:1-300000') |> zoom(resolution = 1000) |> @@ -439,11 +460,12 @@Diamond insulati getBorders() #> Going through preflight checklist... #> Scan each window and compute diamond insulation score... -#> Annotating diamond score prominence for each window... -hic +#> Annotating diamond score prominence for each window...
++hic #> `HiCExperiment` object with 146,812 contacts over 300 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/8ee50b5962e_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/115453d59c5e_7752" #> focus: "II:1-300,000" #> resolutions(5): 1000 2000 4000 8000 16000 #> active resolution: 1000 @@ -451,8 +473,9 @@Diamond insulati #> scores(2): count balanced #> topologicalFeatures: compartments(18) borders(17) loops(0) viewpoints(0) #> pairsFile: N/A -#> metadata(2): eigens insulation - +#> metadata(2): eigens insulation
@@ -464,11 +487,12 @@+# - Export insulation as bigwig track and borders as bed file export(IRanges::coverage(metadata(hic)$insulation, weight = 'insulation'), 'insulation.bw') export(topologicalFeatures(hic, 'borders'), 'borders.bed')Contact map analysis
Virtual 4C
-@@ -700,7 +713,7 @@++mcool_file <- HiContactsData('mESCs', format = 'mcool') #> see ?HiContactsData and browseVignettes('HiContactsData') for documentation -#> loading from cache -hic <- import(mcool_file, format = 'mcool', focus = 'chr18:20000000-35000000', resolution = 40000) +#> loading from cache+hic <- import(mcool_file, format = 'mcool', focus = 'chr18:20000000-35000000', resolution = 40000) v4C <- virtual4C(hic, viewpoint = GRanges('chr18:31000000-31050000')) plot4C(v4C, ggplot2::aes(x = center, y = score))@@ -476,11 +500,12 @@
Virtual 4C
Cis-trans ratios
-++mcool_file <- HiContactsData('yeast_wt', format = 'mcool') #> see ?HiContactsData and browseVignettes('HiContactsData') for documentation -#> loading from cache -hic <- import(mcool_file, format = 'mcool', resolution = 1000) +#> loading from cache+hic <- import(mcool_file, format = 'mcool', resolution = 1000) cisTransRatio(hic) #> # A tibble: 16 × 6 #> # Groups: chr [16] @@ -506,33 +531,40 @@Cis-trans ratios
P(s)
-+++# Without a pairs file mcool_file <- HiContactsData('yeast_wt', format = 'mcool') #> see ?HiContactsData and browseVignettes('HiContactsData') for documentation -#> loading from cache -hic <- import(mcool_file, format = 'mcool', resolution = 1000) +#> loading from cache+#> pairsFile not specified. The P(s) curve will be an approximation.+hic <- import(mcool_file, format = 'mcool', resolution = 1000) ps <- distanceLaw(hic) -#> pairsFile not specified. The P(s) curve will be an approximation. -plotPs(ps, ggplot2::aes(x = binned_distance, y = norm_p)) -#> Warning: Removed 18 rows containing missing values (`geom_line()`).+plotPs(ps, ggplot2::aes(x = binned_distance, y = norm_p)) +#> Warning: Removed 18 rows containing missing values or values outside the scale range +#> (`geom_line()`).-
+++#> loading from cache# With a pairs file pairsFile(hic) <- HiContactsData('yeast_wt', format = 'pairs.gz') #> see ?HiContactsData and browseVignettes('HiContactsData') for documentation -#> loading from cache -ps <- distanceLaw(hic) -#> Importing pairs file /github/home/.cache/R/ExperimentHub/8ee58afa06e_7753 in memory. This may take a while... -plotPs(ps, ggplot2::aes(x = binned_distance, y = norm_p)) -#> Warning: Removed 67 rows containing missing values (`geom_line()`).++ps <- distanceLaw(hic) +#> Importing pairs file /github/home/.cache/R/ExperimentHub/115415055909_7753 in memory. This may take a while...+plotPs(ps, ggplot2::aes(x = binned_distance, y = norm_p)) +#> Warning: Removed 67 rows containing missing values or values outside the scale range +#> (`geom_line()`).-
++#> Warning: Removed 67 rows containing missing values or values outside the scale range +#> (`geom_line()`).plotPsSlope(ps, ggplot2::aes(x = binned_distance, y = slope)) -#> Warning: Removed 67 rows containing missing values (`geom_line()`).-
++# Comparing P(s) curves c1 <- import( @@ -544,8 +576,9 @@P(s) #> see ?HiContactsData and browseVignettes('HiContactsData') for documentation #> loading from cache #> see ?HiContactsData and browseVignettes('HiContactsData') for documentation -#> loading from cache -c2 <- import( +#> loading from cache
++c2 <- import( HiContactsData('yeast_eco1', format = 'mcool'), format = 'mcool', resolution = 1000, @@ -554,29 +587,34 @@P(s) #> see ?HiContactsData and browseVignettes('HiContactsData') for documentation #> loading from cache #> see ?HiContactsData and browseVignettes('HiContactsData') for documentation -#> loading from cache -ps_1 <- distanceLaw(c1) |> mutate(sample = 'WT') -#> Importing pairs file /github/home/.cache/R/ExperimentHub/8ee58afa06e_7753 in memory. This may take a while... -ps_2 <- distanceLaw(c2) |> mutate(sample = 'Eco1-AID') -#> Importing pairs file /github/home/.cache/R/ExperimentHub/8eedb59f3b_7755 in memory. This may take a while... -ps <- rbind(ps_1, ps_2) +#> loading from cache
++ps_1 <- distanceLaw(c1) |> mutate(sample = 'WT') +#> Importing pairs file /github/home/.cache/R/ExperimentHub/115415055909_7753 in memory. This may take a while...++ps_2 <- distanceLaw(c2) |> mutate(sample = 'Eco1-AID') +#> Importing pairs file /github/home/.cache/R/ExperimentHub/11544471e734_7755 in memory. This may take a while...+#> Warning: Removed 134 rows containing missing values or values outside the scale range +#> (`geom_line()`).+ps <- rbind(ps_1, ps_2) plotPs(ps, ggplot2::aes(x = binned_distance, y = norm_p, group = sample, color = sample)) -#> Warning: Removed 134 rows containing missing values (`geom_line()`).-
++#> Warning: Removed 135 rows containing missing values or values outside the scale range +#> (`geom_line()`).plotPsSlope(ps, ggplot2::aes(x = binned_distance, y = slope, group = sample, color = sample)) -#> Warning: Removed 135 rows containing missing values (`geom_line()`).
Session info
-++#> [1] strawr_0.0.91 rstudioapi_0.16.0 jsonlite_1.8.8 +#> [4] magrittr_2.0.3 ggbeeswarm_0.7.2 farver_2.1.2 +#> [7] rmarkdown_2.27 fs_1.6.4 BiocIO_1.15.0 +#> [10] zlibbioc_1.51.0 ragg_1.3.2 vctrs_0.6.5 +#> [13] memoise_2.0.1 Cairo_1.6-2 Rsamtools_2.21.0 +#> [16] RCurl_1.98-1.14 terra_1.7-78 base64enc_0.1-3 +#> [19] htmltools_0.5.8.1 S4Arrays_1.5.1 dynamicTreeCut_1.63-1 +#> [22] curl_5.2.1 Rhdf5lib_1.27.0 Formula_1.2-5 +#> [25] SparseArray_1.5.7 rhdf5_2.49.0 sass_0.4.9 +#> [28] bslib_0.7.0 htmlwidgets_1.6.4 desc_1.4.3 +#> [31] impute_1.79.0 cachem_1.1.0 GenomicAlignments_1.41.0 +#> [34] mime_0.12 lifecycle_1.0.4 iterators_1.0.14 +#> [37] pkgconfig_2.0.3 Matrix_1.7-0 R6_2.5.1 +#> [40] fastmap_1.2.0 GenomeInfoDbData_1.2.12 digest_0.6.35 +#> [43] colorspace_2.1-0 patchwork_1.2.0 AnnotationDbi_1.67.0 +#> [46] RSpectra_0.16-1 Hmisc_5.1-3 textshaping_0.4.0 +#> [49] RSQLite_2.3.7 filelock_1.0.3 labeling_0.4.3 +#> [52] fansi_1.0.6 httr_1.4.7 abind_1.4-5 +#> [55] compiler_4.4.0 bit64_4.0.5 withr_3.0.0 +#> [58] doParallel_1.0.17 backports_1.5.0 htmlTable_2.4.2 +#> [61] BiocParallel_1.39.0 DBI_1.2.3 highr_0.11 +#> [64] rappdirs_0.3.3 DelayedArray_0.31.1 rjson_0.2.21 +#> [67] tools_4.4.0 foreign_0.8-86 vipor_0.4.7 +#> [70] beeswarm_0.4.0 nnet_7.3-19 glue_1.7.0 +#> [73] restfulr_0.0.15 rhdf5filters_1.17.0 grid_4.4.0 +#> [76] checkmate_2.3.1 cluster_2.1.6 generics_0.1.3 +#> [79] gtable_0.3.5 tzdb_0.4.0 preprocessCore_1.67.0 +#> [82] tidyr_1.3.1 data.table_1.15.4 hms_1.1.3 +#> [85] WGCNA_1.72-5 utf8_1.2.4 XVector_0.45.0 +#> [88] BiocVersion_3.20.0 foreach_1.5.2 pillar_1.9.0 +#> [91] stringr_1.5.1 vroom_1.6.5 splines_4.4.0 +#> [94] lattice_0.22-6 survival_3.6-4 bit_4.0.5 +#> [97] tidyselect_1.2.1 GO.db_3.19.1 Biostrings_2.73.0 +#> [100] knitr_1.47 gridExtra_2.3 bookdown_0.39 +#> [103] xfun_0.44 stringi_1.8.4 UCSC.utils_1.1.0 +#> [106] yaml_2.3.8 evaluate_0.23 codetools_0.2-20 +#> [109] tibble_3.2.1 BiocManager_1.30.23 cli_3.6.2 +#> [112] rpart_4.1.23 systemfonts_1.1.0 munsell_0.5.1 +#> [115] jquerylib_0.1.4 Rcpp_1.0.12 png_0.1-8 +#> [118] fastcluster_1.2.6 XML_3.99-0.16.1 ggrastr_1.0.2 +#> [121] parallel_4.4.0 pkgdown_2.0.9 readr_2.1.5 +#> [124] blob_1.2.4 bitops_1.0-7 scales_1.3.0 +#> [127] purrr_1.0.2 crayon_1.5.2 rlang_1.1.3 +#> [130] KEGGREST_1.45.0sessionInfo() -#> R Under development (unstable) (2023-11-14 r85524) +#> R version 4.4.0 (2024-04-24) #> Platform: x86_64-pc-linux-gnu -#> Running under: Ubuntu 22.04.3 LTS +#> Running under: Ubuntu 22.04.4 LTS #> #> Matrix products: default #> BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 @@ -598,88 +636,63 @@Session info#> [8] base #> #> other attached packages: -#> [1] InteractionSet_1.31.0 SummarizedExperiment_1.33.0 -#> [3] Biobase_2.63.0 MatrixGenerics_1.15.0 -#> [5] matrixStats_1.1.0 rtracklayer_1.63.0 -#> [7] HiContacts_1.3.2 HiContactsData_1.5.0 -#> [9] ExperimentHub_2.11.0 AnnotationHub_3.11.0 -#> [11] BiocFileCache_2.11.1 dbplyr_2.4.0 -#> [13] HiCExperiment_1.3.0 GenomicRanges_1.55.1 -#> [15] GenomeInfoDb_1.39.1 IRanges_2.37.0 -#> [17] S4Vectors_0.41.1 BiocGenerics_0.49.1 -#> [19] dplyr_1.1.4 ggplot2_3.4.4 -#> [21] BiocStyle_2.31.0 +#> [1] InteractionSet_1.33.0 SummarizedExperiment_1.35.0 +#> [3] Biobase_2.65.0 MatrixGenerics_1.17.0 +#> [5] matrixStats_1.3.0 rtracklayer_1.65.0 +#> [7] HiContacts_1.5.0 HiContactsData_1.7.0 +#> [9] ExperimentHub_2.13.0 AnnotationHub_3.13.0 +#> [11] BiocFileCache_2.13.0 dbplyr_2.5.0 +#> [13] HiCExperiment_1.5.0 GenomicRanges_1.57.0 +#> [15] GenomeInfoDb_1.41.1 IRanges_2.39.0 +#> [17] S4Vectors_0.43.0 BiocGenerics_0.51.0 +#> [19] dplyr_1.1.4 ggplot2_3.5.1 +#> [21] BiocStyle_2.33.0 #> #> loaded via a namespace (and not attached): -#> [1] splines_4.4.0 later_1.3.1 -#> [3] BiocIO_1.13.0 bitops_1.0-7 -#> [5] filelock_1.0.2 tibble_3.2.1 -#> [7] preprocessCore_1.65.0 XML_3.99-0.15 -#> [9] rpart_4.1.21 lifecycle_1.0.4 -#> [11] fastcluster_1.2.3 doParallel_1.0.17 -#> [13] rprojroot_2.0.4 lattice_0.22-5 -#> [15] vroom_1.6.4 backports_1.4.1 -#> [17] magrittr_2.0.3 Hmisc_5.1-1 -#> [19] sass_0.4.7 rmarkdown_2.25 -#> [21] jquerylib_0.1.4 yaml_2.3.7 -#> [23] httpuv_1.6.12 DBI_1.1.3 -#> [25] abind_1.4-5 zlibbioc_1.49.0 -#> [27] purrr_1.0.2 RCurl_1.98-1.13 -#> [29] nnet_7.3-19 rappdirs_0.3.3 -#> [31] GenomeInfoDbData_1.2.11 terra_1.7-55 -#> [33] RSpectra_0.16-1 pkgdown_2.0.7 -#> [35] codetools_0.2-19 DelayedArray_0.29.0 -#> [37] tidyselect_1.2.0 farver_2.1.1 -#> [39] dynamicTreeCut_1.63-1 base64enc_0.1-3 -#> [41] GenomicAlignments_1.39.0 jsonlite_1.8.7 -#> [43] ellipsis_0.3.2 Formula_1.2-5 -#> [45] survival_3.5-7 iterators_1.0.14 -#> [47] systemfonts_1.0.5 foreach_1.5.2 -#> [49] tools_4.4.0 ragg_1.2.6 -#> [51] strawr_0.0.91 Rcpp_1.0.11 -#> [53] glue_1.6.2 gridExtra_2.3 -#> [55] SparseArray_1.3.1 xfun_0.41 -#> [57] withr_2.5.2 BiocManager_1.30.22 -#> [59] fastmap_1.1.1 rhdf5filters_1.15.1 -#> [61] fansi_1.0.5 digest_0.6.33 -#> [63] R6_2.5.1 mime_0.12 -#> [65] textshaping_0.3.7 colorspace_2.1-0 -#> [67] GO.db_3.18.0 Cairo_1.6-1 -#> [69] RSQLite_2.3.3 utf8_1.2.4 -#> [71] tidyr_1.3.0 generics_0.1.3 -#> [73] data.table_1.14.8 httr_1.4.7 -#> [75] htmlwidgets_1.6.2 S4Arrays_1.3.0 -#> [77] pkgconfig_2.0.3 gtable_0.3.4 -#> [79] blob_1.2.4 impute_1.77.0 -#> [81] XVector_0.43.0 htmltools_0.5.7 -#> [83] bookdown_0.36 scales_1.2.1 -#> [85] png_0.1-8 knitr_1.45 -#> [87] rstudioapi_0.15.0 tzdb_0.4.0 -#> [89] rjson_0.2.21 checkmate_2.3.0 -#> [91] curl_5.1.0 cachem_1.0.8 -#> [93] rhdf5_2.47.0 stringr_1.5.1 -#> [95] BiocVersion_3.19.1 parallel_4.4.0 -#> [97] vipor_0.4.5 foreign_0.8-85 -#> [99] AnnotationDbi_1.65.2 ggrastr_1.0.2 -#> [101] restfulr_0.0.15 desc_1.4.2 -#> [103] pillar_1.9.0 grid_4.4.0 -#> [105] vctrs_0.6.4 promises_1.2.1 -#> [107] xtable_1.8-4 cluster_2.1.4 -#> [109] beeswarm_0.4.0 htmlTable_2.4.2 -#> [111] evaluate_0.23 readr_2.1.4 -#> [113] cli_3.6.1 compiler_4.4.0 -#> [115] Rsamtools_2.19.2 rlang_1.1.2 -#> [117] crayon_1.5.2 labeling_0.4.3 -#> [119] fs_1.6.3 ggbeeswarm_0.7.2 -#> [121] stringi_1.8.1 WGCNA_1.72-1 -#> [123] BiocParallel_1.37.0 munsell_0.5.0 -#> [125] Biostrings_2.71.1 Matrix_1.6-3 -#> [127] hms_1.1.3 patchwork_1.1.3 -#> [129] bit64_4.0.5 Rhdf5lib_1.25.0 -#> [131] KEGGREST_1.43.0 shiny_1.8.0 -#> [133] interactiveDisplayBase_1.41.0 highr_0.10 -#> [135] memoise_2.0.1 bslib_0.5.1 -#> [137] bit_4.0.5
Session info -
Site built with pkgdown 2.0.7.
+Site built with pkgdown 2.0.9.
Articles • HiContacts Articles • HiContacts @@ -17,7 +17,7 @@All vignettes
Authors and Citation • HiContacts Authors and Citation • HiContacts @@ -17,7 +17,7 @@@@ -84,7 +87,7 @@Citation
Analysing cool files in R with HiContacts • HiContacts - + - +Contacts — Contacts • HiContacts Contacts — Contacts • HiContacts HiContacts plotting functionalities — HiContacts-plots • HiContacts HiContacts plotting functionalities
Compute the law of distance-dependent contact frequency, a.k.a. P(s) — distanceLaw • HiContacts HiContacts arithmetics functionalities — arithmetics • HiContacts HiContacts arithmetics functionalities — arithmetics • HiContacts HiContacts - 1.3.2 + 1.5.0Examples
#> #> `HiCExperiment` object with 8,757,906 contacts over 763 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/8ee50b5962e_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/115453d59c5e_7752" #> focus: "whole genome" #> resolutions(5): 1000 2000 4000 8000 16000 #> active resolution: 16000 @@ -251,7 +251,7 @@Examples
detrend(contacts_yeast) #> `HiCExperiment` object with 8,757,906 contacts over 763 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/8ee50b5962e_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/115453d59c5e_7752" #> focus: "whole genome" #> resolutions(5): 1000 2000 4000 8000 16000 #> active resolution: 16000 @@ -269,7 +269,7 @@Examples
#> #> `HiCExperiment` object with 8,757,906 contacts over 763 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/8ee50b5962e_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/115453d59c5e_7752" #> focus: "whole genome" #> resolutions(5): 1000 2000 4000 8000 16000 #> active resolution: 16000 @@ -307,7 +307,7 @@Examples
merge(contacts_yeast_eco1, contacts_yeast) #> `HiCExperiment` object with 733,836.5 contacts over 51 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/8ee79d66ed6_7754" +#> fileName: "/github/home/.cache/R/ExperimentHub/1154359fc54_7754" #> focus: "II" #> resolutions(5): 1000 2000 4000 8000 16000 #> active resolution: 16000 @@ -324,7 +324,7 @@Examples
despeckle(contacts_yeast) #> `HiCExperiment` object with 471,364 contacts over 51 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/8ee50b5962e_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/115453d59c5e_7752" #> focus: "II" #> resolutions(5): 1000 2000 4000 8000 16000 #> active resolution: 16000 @@ -349,7 +349,7 @@Examples
#> Filtering for contacts within provided targets... #> `AggrHiCExperiment` object over 16 targets #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/8ee50b5962e_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/115453d59c5e_7752" #> focus: 16 targets #> resolutions(5): 1000 2000 4000 8000 16000 #> active resolution: 1000 @@ -370,7 +370,7 @@Examples
boost(contacts, alpha = 1) #> `HiCExperiment` object with 469,569 contacts over 814 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/8ee50b5962e_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/115453d59c5e_7752" #> focus: "II" #> resolutions(5): 1000 2000 4000 8000 16000 #> active resolution: 1000 @@ -400,7 +400,7 @@Examples
Checks functions — checks • HiContacts Checks functions — checks • HiContacts cisTransRatio — cisTransRatio • HiContacts cisTransRatio — cisTransRatio • HiContacts @@ -17,7 +17,7 @@Examples
Contact map compartments — getCompartments • HiContacts Contact map compartments — getCompartments • HiContacts Contact map insulation — getDiamondInsulation • HiContacts Contact map insulation — getDiamondInsulation • HiContacts @@ -17,7 +17,7 @@Examples
#> Annotating diamond score prominence for each window... #> `HiCExperiment` object with 146,812 contacts over 300 regions #> ------- -#> fileName: "/github/home/.cache/R/ExperimentHub/8ee50b5962e_7752" +#> fileName: "/github/home/.cache/R/ExperimentHub/115453d59c5e_7752" #> focus: "II:1-300,000" #> resolutions(5): 1000 2000 4000 8000 16000 #> active resolution: 1000 @@ -132,7 +132,7 @@Examples
Finding loops in contact map — getLoops • HiContacts Finding loops in contact map — getLoops • HiContacts Function reference • HiContacts Function reference • HiContacts @@ -17,7 +17,7 @@All functions
Matrix palettes — palettes • HiContacts Matrix palettes — palettes • HiContacts @@ -17,7 +17,7 @@
Examples
diff --git a/reference/plot4C-1.png b/reference/plot4C-1.png index c5f0681..ae61a6c 100644 Binary files a/reference/plot4C-1.png and b/reference/plot4C-1.png differ diff --git a/reference/plot4C.html b/reference/plot4C.html index cc147d1..ca67a90 100644 --- a/reference/plot4C.html +++ b/reference/plot4C.html @@ -1,5 +1,5 @@ -Examples
diff --git a/reference/plotMatrix-1.png b/reference/plotMatrix-1.png index dc4c022..20c1355 100644 Binary files a/reference/plotMatrix-1.png and b/reference/plotMatrix-1.png differ diff --git a/reference/plotMatrix.html b/reference/plotMatrix.html index 2323e3d..4109549 100644 --- a/reference/plotMatrix.html +++ b/reference/plotMatrix.html @@ -1,5 +1,5 @@ -Examples
diff --git a/reference/plotPs-1.png b/reference/plotPs-1.png index 5d620a7..fdf896d 100644 Binary files a/reference/plotPs-1.png and b/reference/plotPs-1.png differ diff --git a/reference/plotPs-2.png b/reference/plotPs-2.png index 69f080c..cf7f548 100644 Binary files a/reference/plotPs-2.png and b/reference/plotPs-2.png differ diff --git a/reference/plotPs-3.png b/reference/plotPs-3.png index 0762c17..1587a12 100644 Binary files a/reference/plotPs-3.png and b/reference/plotPs-3.png differ diff --git a/reference/plotPs.html b/reference/plotPs.html index 09c356b..2687e2f 100644 --- a/reference/plotPs.html +++ b/reference/plotPs.html @@ -1,5 +1,5 @@ -Examples
ps <- distanceLaw(contacts_yeast) #> pairsFile not specified. The P(s) curve will be an approximation. plotPs(ps, ggplot2::aes(x = binned_distance, y = norm_p)) -#> Warning: Removed 13 rows containing missing values (`geom_line()`). +#> Warning: Removed 13 rows containing missing values or values outside the scale range +#> (`geom_line()`).
## Comparing several P(s)
@@ -112,10 +113,12 @@ Examples
ps_eco1$sample <- 'eco1' ps <- rbind(ps_wt, ps_eco1) plotPs(ps, ggplot2::aes(x = binned_distance, y = norm_p, group = sample, color = sample)) -#> Warning: Removed 26 rows containing missing values (`geom_line()`). +#> Warning: Removed 26 rows containing missing values or values outside the scale range +#> (`geom_line()`).
plotPsSlope(ps, ggplot2::aes(x = binned_distance, y = slope, group = sample))
-#> Warning: Removed 26 rows containing missing values (`geom_line()`).
+#> Warning: Removed 26 rows containing missing values or values outside the scale range
+#> (`geom_line()`).
@@ -131,7 +134,7 @@ Examples
diff --git a/reference/plotSaddle.html b/reference/plotSaddle.html index ced88bc..5df6361 100644 --- a/reference/plotSaddle.html +++ b/reference/plotSaddle.html @@ -1,5 +1,5 @@ -Value
diff --git a/reference/plotScalogram-1.png b/reference/plotScalogram-1.png index cb2dc86..b507688 100644 Binary files a/reference/plotScalogram-1.png and b/reference/plotScalogram-1.png differ diff --git a/reference/plotScalogram.html b/reference/plotScalogram.html index c04d6b7..2881377 100644 --- a/reference/plotScalogram.html +++ b/reference/plotScalogram.html @@ -1,5 +1,5 @@ -Examples
#> see ?HiContactsData and browseVignettes('HiContactsData') for documentation #> loading from cache scalo <- scalogram(contacts_yeast['II']) -#> Importing pairs file /github/home/.cache/R/ExperimentHub/8ee58afa06e_7753 in memory. This may take a while... +#> Importing pairs file /github/home/.cache/R/ExperimentHub/115415055909_7753 in memory. This may take a while... plotScalogram(scalo)
@@ -101,7 +101,7 @@