diff --git a/ChangeLog b/ChangeLog index 84c7e318..80d92c22 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,796 @@ +* 2024-10-12(Tal Galili) Fixes issue #126 (linewidth in heatmaply not respected) |cf49949| +| R/ggdend.R | 2 +- +| 1 file changed, 1 insertion(+), 1 deletion(-) + +* 2024-10-05(Tal Galili) Update citation URL to use DOI |950afec| +| DESCRIPTION | 2 +- +| README.md | 2 +- +| docs/authors.html | 2 +- +| inst/CITATION | 2 +- +| 4 files changed, 4 insertions(+), 4 deletions(-) + +* 2024-10-05(Tal Galili) Fix redirect url |a4c6206| +| README.md | 2 +- +| docs/authors.html | 2 +- +| inst/CITATION | 2 +- +| 3 files changed, 3 insertions(+), 3 deletions(-) + +* 2024-10-05(Tal Galili) Fix NEWS.rmd and update pkgdown |b85fc40| +| DESCRIPTION | 2 +- +| NEWS.md | 618 ++--- +| docs/404.html | 20 +- +| docs/CONDUCT.html | 20 +- +| docs/articles/Cluster_Analysis.html | 1213 +++++---- +| .../figure-html/unnamed-chunk-11-1.png | Bin 194462 -> 195786 bytes +| 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files changed, 5 insertions(+), 1482 deletions(-) + +* 2024-09-24(Tal Galili) Updating yaml for code coverage. |586b59c| +| .github/workflows/test-coverage.yaml | 27 +++++++++++++++++++-------- +| 1 file changed, 19 insertions(+), 8 deletions(-) + +* 2024-09-24(Tal Galili) Update DESCRIPTION and NEWS |0f15497| +| DESCRIPTION | 2 +- +| NEWS | 9 +++++---- +| NEWS.md | 9 +++++---- +| R/zzz.R | 2 +- +| 4 files changed, 12 insertions(+), 10 deletions(-) + +* 2024-09-24(alecbuetow) Fixed rect.dendogram 2 rectangle bug (#124) |370e535| +| R/rect.dendrogram.R | 6 +++--- +| 1 file changed, 3 insertions(+), 3 deletions(-) + +* 2024-09-23(alecbuetow) Added 2 Tests for Untangle.R (#123) |36b035b| +| tests/testthat/test-untangle.R | 44 ++++++++++++++++++++++++++++++++++++++++ +| 1 file changed, 44 insertions(+) + +* 2024-08-31(Tal Galili) Update docs and NEWS to 1.18.0 |f5c5d0b| +| DESCRIPTION | 2 +- +| NAMESPACE | 8 +++++--- +| NEWS | 11 +++-------- +| NEWS.md | 11 +++++++++-- +| R/untangle.R | 12 +++++++----- +| man/untangle.Rd | 12 +++++++----- +| 6 files changed, 32 insertions(+), 24 deletions(-) + +* 2024-08-31(Tal Galili) Stop tracking linter for the time being |d906461| +| .github/workflows/lint.yaml | 2 +- +| 1 file changed, 1 insertion(+), 1 deletion(-) + +* 2024-08-31(Tal Galili) Remove windoes r: 4.1 check (since it seems to fail on installing Hmisc for some reason) |6eb3b3a| +| .github/workflows/R-CMD-check.yaml | 1 - +| 1 file changed, 1 deletion(-) + +* 2024-08-31(Tal Galili) Trying to fix the Hmisc error |7eaa20d| +| .github/workflows/R-CMD-check.yaml | 13 ++----------- +| 1 file changed, 2 insertions(+), 11 deletions(-) + +* 2024-08-31(Tal Galili) Update untangle_step_rotate_both_side to not need dplyr |67355f7| +| tests/testthat/test-untangle.R | 17 +++++++++++------ +| 1 file changed, 11 insertions(+), 6 deletions(-) + +* 2024-08-31(Tal Galili) Fix warnings in tests and roxygen2 |c65d34c| +| .gitignore | 4 ++- +| NAMESPACE | 9 +++--- +| R/dendextend-package.R | 2 +- +| R/entanglement.R | 1 + +| R/ggdend.R | 61 +++++++++++++++++++++----------------- +| tests/{test-all.R => testthat.R} | 2 +- +| tests/testthat/test-ggdend.R | 8 ++--- +| 7 files changed, 47 insertions(+), 40 deletions(-) + +* 2024-08-31(Tal Galili) Fix untange test failure |3c2d436| +| tests/testthat/test-untangle.R | 7 ++++--- +| 1 file changed, 4 insertions(+), 3 deletions(-) + +* 2024-08-31(Tal Galili) Fix tests to be able to run again |ef919e1| +| tests/testthat/test-attr_access.R | 2 +- +| 1 file changed, 1 insertion(+), 1 deletion(-) + +* 2024-08-31(alecbuetow) Added stepBothSides algorithm to untangle methods (#122) |d4d6530| +| DESCRIPTION | 5 +- +| NAMESPACE | 1 + +| NEWS | 6 ++ +| R/untangle.R | 133 +++++++++++++++++++++++++++++++- +| man/dendextend-package.Rd | 41 ++++++++++ +| man/untangle.Rd | 3 +- +| man/untangle_step_rotate_both_side.Rd | 108 ++++++++++++++++++++++++++ +| tests/testthat/test-untangle.R | 26 ++++++- +| 8 files changed, 317 insertions(+), 6 deletions(-) + +* 2023-12-16(Tal Galili) Another attempt to deal with Hmisc installation |278999b| +| .github/workflows/R-CMD-check.yaml | 12 ++++++++---- +| 1 file changed, 8 insertions(+), 4 deletions(-) + +* 2023-12-16(Tal Galili) Try another R-CMD-check.yaml file - try 2 |402ce1d| +| .github/workflows/R-CMD-check.yaml | 25 ++++++++++++------------- +| 1 file changed, 12 insertions(+), 13 deletions(-) + +* 2023-12-16(Tal Galili) Try another R-CMD-check.yaml file |5435367| +| .github/workflows/R-CMD-check.yaml | 18 +++--------------- +| 1 file changed, 3 insertions(+), 15 deletions(-) + +* 2023-12-16(Tal Galili) Add tests to attr_access |82c908b| +| tests/testthat/test-attr_access.R | 82 +++++++++++++++++++++++++++++++++++++ +| 1 file changed, 82 insertions(+) + +* 2023-12-16(Tal Galili) Remove broken test |fcd3eae| +| tests/testthat/test-ggdend.R | 9 --------- +| 1 file changed, 9 deletions(-) + +* 2023-12-16(Tal Galili) Add tests to ggdend |a82de2b| +| tests/testthat/test-ggdend.R | 92 ++++++++++++++++++++++++++++++++++++++++++ +| 1 file changed, 92 insertions(+) + +* 2023-12-16(Tal Galili) Add and update tests for get_nodes_xy function |96bc5cd| +| DESCRIPTION | 4 ++-- +| NEWS | 6 ++++++ +| tests/testthat/test-get_nodes_xy.R | 41 ++++++++++++++++++++++++++++++++++++ +| 3 files changed, 49 insertions(+), 2 deletions(-) + +* 2023-03-31(Tal Galili) Fix type in missing seriation package message |c1f8608| +| R/seriate_dendrogram.R | 2 +- +| 1 file changed, 1 insertion(+), 1 deletion(-) + +* 2023-03-25(Tal Galili) Fix misc 500 error in a url |dcf42ee| +| vignettes/dendextend.Rmd | 2 +- +| 1 file changed, 1 insertion(+), 1 deletion(-) + +* 2023-03-25(Tal Galili) Remove "https://www.r-statistics.com" from being directly linked to |c76aa00| +| vignettes/dendextend.Rmd | 2 +- +| 1 file changed, 1 insertion(+), 1 deletion(-) + +* 2023-03-25(Tal Galili) Fix misc url issues |8991549| +| DESCRIPTION | 4 ++-- +| NEWS | 6 ++++++ +| NEWS.md | 6 ++++++ +| README.md | 1 - +| docs/404.html | 4 ++-- +| docs/CONDUCT.html | 4 ++-- +| docs/authors.html | 4 ++-- +| docs/index.html | 6 +++--- +| docs/news/index.html | 23 ++++++++++++++++++----- +| vignettes/dendextend.Rmd | 2 +- +| 10 files changed, 42 insertions(+), 18 deletions(-) + +* 2023-03-24(Tal Galili) Update github workflows to use v2 |7a9c4e5| +| .github/workflows/R-CMD-check.yaml | 31 +++++++++++++++++++++++++++---- +| .github/workflows/check-release.yaml | 25 +++++++------------------ +| .github/workflows/check-standard.yaml | 29 ++++++++++------------------- +| .github/workflows/lint.yaml | 13 ++++++++----- +| .github/workflows/pkgdown.yaml | 33 ++++++++++++++++++++++----------- +| .github/workflows/pr-commands.yaml | 4 ++-- +| .github/workflows/test-coverage.yaml | 32 ++++++++++++++++++++++++++------ +| R/zzz.R | 4 ++++ +| 8 files changed, 106 insertions(+), 65 deletions(-) + +* 2023-03-24(Tal Galili) Fix "Cannot process chunk/lines:" in the NEWS file |e568c21| +| NEWS | 17 +++-------------- +| NEWS.md | 15 +++++++++++++-- +| 2 files changed, 16 insertions(+), 16 deletions(-) + +* 2023-03-24(Tal Galili) Fixed: "Package CITATION file contains call(s) to old-style citEntry(). Please use bibentry() instead." |e5c594f| +| NEWS | 2 ++ +| inst/CITATION | 17 +++++++---------- +| 2 files changed, 9 insertions(+), 10 deletions(-) + +* 2023-03-24(Tal Galili) Fix ggplot.ggdend S3 generic/method consistency |5865a99| +| DESCRIPTION | 6 +++--- +| NEWS | 18 +++++++++++++++--- +| R/ggdend.R | 9 ++++++--- +| man/ggdend.Rd | 10 ++++++++-- +| man/set.Rd | 16 ++++++++-------- +| 5 files changed, 40 insertions(+), 19 deletions(-) + +* 2022-11-01(Tal Galili) document elipsis |a52e7d7| +| R/get_subdendrograms.R | 1 + +| man/collapse_labels.Rd | 2 ++ +| 2 files changed, 3 insertions(+) + +* 2022-11-01(Tal Galili) Add tests to collapse_labels |d6899eb| +| tests/testthat/test-get_subdendrograms.R | 27 ++++++++++++++++++++++++++- +| 1 file changed, 26 insertions(+), 1 deletion(-) + +* 2022-11-01(Tal Galili) Added the collapse_labels function |eb8fa9b| +| DESCRIPTION | 4 +-- +| NAMESPACE | 1 + +| NEWS | 8 +++++ +| R/get_subdendrograms.R | 79 ++++++++++++++++++++++++++++++++++++++++++++++++ +| man/collapse_labels.Rd | 45 +++++++++++++++++++++++++++ +| 5 files changed, 135 insertions(+), 2 deletions(-) + +* 2022-10-08(Tal Galili) update github actions |0a53957| +| .github/workflows/R-CMD-check.yaml | 49 ++++++++++++++++++++++++++++++++++++ +| .github/workflows/pr-commands.yaml | 28 ++++++++++++--------- +| README.md | 3 +++ +| 3 files changed, 68 insertions(+), 12 deletions(-) + +* 2022-08-06(Tal Galili) Add github actions |87b55e1| +| .github/workflows/check-release.yaml | 40 ++++++++++++++++++ +| .github/workflows/check-standard.yaml | 58 +++++++++++++++++++++++++ +| .github/workflows/lint.yaml | 29 +++++++++++++ +| .github/workflows/pr-commands.yaml | 75 +++++++++++++++++++++++++++++++++ +| .github/workflows/test-coverage.yaml | 30 +++++++++++++ +| 5 files changed, 232 insertions(+) + +* 2022-08-06(Tal Galili) Added usethis::use_github_action("pkgdown") |74b9d01| +| .github/.gitignore | 1 + +| .github/workflows/pkgdown.yaml | 35 +++++++++++++++++++++++++++++++++++ +| 2 files changed, 36 insertions(+) + +* 2022-07-16(Tal Galili) Some updating on the pkgdown |f02d7b3| +| docs/pkgdown.yml | 2 +- +| docs/reference/FM_index_permutation.html | 10 ++++----- +| docs/reference/Rplot001.png | Bin 7062 -> 4480 bytes +| docs/reference/Rplot002.png | Bin 9877 -> 4588 bytes +| docs/reference/Rplot003.png | Bin 11879 -> 9529 bytes +| docs/reference/Rplot004.png | Bin 14430 -> 10574 bytes +| docs/reference/Rplot005.png | Bin 22110 -> 7394 bytes +| docs/reference/Rplot006.png | Bin 9450 -> 49630 bytes +| docs/reference/Rplot007.png | Bin 34304 -> 5468 bytes +| docs/reference/Rplot008.png | Bin 37110 -> 49630 bytes +| docs/reference/khan.html | 34 ++++++++++++++--------------- +| 11 files changed, 22 insertions(+), 24 deletions(-) + +* 2022-07-04(Tal Galili) Fix: |70b6e03| +| DESCRIPTION | 2 +- +| NEWS | 4 ++-- +| NEWS.md | 4 ++-- +| R/data.R | 34 +++++++++++++++++----------------- +| 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vignettes/Cluster_Analysis.Rmd | 2 +- +| 155 files changed, 14740 insertions(+), 25740 deletions(-) + +* 2022-07-03(Tal Galili) Update log files |172e35a| +| ChangeLog | 117 +++++++++++++++++++++++++++++++++++++++++++++++++++++------- +| NEWS.md | 18 ++++++++++ +| R/zzz.R | 1 + +| README.md | 7 ++-- +| 4 files changed, 129 insertions(+), 14 deletions(-) + * 2022-07-03(Tal Galili) comment out library(zoo) - to let pkgdown run properly. |6b87e9e| | R/pvclust.R | 21 +++++++++++---------- | man/na_locf.Rd | 25 +++++++++++++------------ @@ -70,7 +863,7 @@ | | R/ggdend.R | 8 ++++---- | | 1 file changed, 4 insertions(+), 4 deletions(-) -* | 2021-10-27(Tal Galili) update NEWS |3daf4af +* / 2021-10-27(Tal Galili) update NEWS |3daf4af |/ | | DESCRIPTION | 2 +- | NEWS | 5 ++++- @@ -1089,7 +1882,7 @@ | | R/ggdend.R | 11 +++++++---- | | 1 file changed, 7 insertions(+), 4 deletions(-) -* | 2020-05-15(Tal Galili) For future spell checking |65b9b67 +* / 2020-05-15(Tal Galili) For future spell checking |65b9b67 |/ | | R/zzz.R | 1 + | inst/WORDLIST | 235 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ diff --git a/DESCRIPTION b/DESCRIPTION index 39d0dadb..4435b9a6 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: dendextend Type: Package Title: Extending 'dendrogram' Functionality in R -Version: 1.18.0 -Date: 2024-10-05 +Version: 1.18.1 +Date: 2024-10-12 Authors@R: c(person("Tal", "Galili", role = c("aut", "cre", "cph"), email = "tal.galili@gmail.com", comment = "https://www.r-statistics.com"), person("Yoav", "Benjamini", email = "ybenja@tau.ac.il",role = "ths"), diff --git a/NEWS.md b/NEWS.md index fed1a946..aac191f1 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,8 @@ +dendextend 1.18.1 (2024-10-12) +============================== +## BUG FIXES +- Fix ggplot.ggdend that didn't respect lwd (see: https://github.com/talgalili/dendextend/issues/126) + dendextend 1.18.0 (2024-10-05) ============================== ## NEW FUNCTION diff --git a/R/zzz.R b/R/zzz.R index 96eeea13..154c2c5a 100644 --- a/R/zzz.R +++ b/R/zzz.R @@ -335,7 +335,6 @@ dendextendWelcomeMessage <- function() { # shell('git log --graph --stat --date=short --pretty=format:"%ad(%an) %s |%h" > ChangeLog', intern = TRUE) # For linux: # system('git log --graph --stat --date=short --pretty=format:"%ad(%an) %s |%h" > ChangeLog', intern = TRUE) -# file.copy("NEWS", "NEWS.md",overwrite = TRUE) # pkgdown::build_site(run_dont_run = FALSE) # pkgdown::build_home() # pkgdown::build_news() diff --git a/docs/404.html b/docs/404.html index 9f8cc18e..17b5db48 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ dendextend - 1.18.0 + 1.18.1 diff --git a/docs/CONDUCT.html b/docs/CONDUCT.html index dc4afc78..b0284e5b 100644 --- a/docs/CONDUCT.html +++ b/docs/CONDUCT.html @@ -17,7 +17,7 @@ dendextend - 1.18.0 + 1.18.1 diff --git a/docs/authors.html b/docs/authors.html index a87f6fdb..930f1692 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ dendextend - 1.18.0 + 1.18.1 diff --git a/docs/index.html b/docs/index.html index 9a0a16f9..76fd657c 100644 --- a/docs/index.html +++ b/docs/index.html @@ -33,7 +33,7 @@ dendextend - 1.18.0 + 1.18.1 @@ -146,7 +146,7 @@

How to cite the dendextend package journal = {Bioinformatics}, year = {2015}, doi = {10.1093/bioinformatics/btv428}, - url = {https://academic.oup.com/bioinformatics/article/31/22/3718/240978/dendextend-an-R-package-for-visualizing-adjusting}, + url = {https://doi.org/10.1093/bioinformatics/btv428}, eprint = {https://academic.oup.com/bioinformatics/article-pdf/31/22/3718/17122682/btv428.pdf}, }

This free open-source software implements academic research by the authors and co-workers. If you use it, please support the project by citing the appropriate journal articles.

diff --git a/docs/news/index.html b/docs/news/index.html index baf36a73..ac545804 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -17,7 +17,7 @@ dendextend - 1.18.0 + 1.18.1 @@ -67,7 +67,14 @@

Changelog

-

dendextend 1.18.0 (2024-10-05)

+

dendextend 1.18.1 (2024-10-12)

+
+

BUG FIXES

+
+
+
+

dendextend 1.18.0 (2024-10-05)2024-10-05

NEW FUNCTION