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Changelog

Source: NEWS.md

TOmicsVis 2.0.0

CRAN release: 2023-08-28

Date: 2023-10-16

New Features:

  1. Paper Publish: TOmicsVis: An All-in-One Transcriptomic Analysis and Visualization R Package with shinyapp Interface

Miao, Ben-Ben, Dong, Wei, Han, Zhao-Fang, Luo, Xuan, Ke, Cai-Huan, and You, Wei-Wei. 2023. “ TOmicsVis: An All-in-One Transcriptomic Analysis and Visualization R Package with shinyapp Interface.” iMeta e137. https://doi.org/10.1002/imt2.137

  1. Citation function: citation(package = "TOmicsVis")

Bugs Fixed:

TOmicsVis 2.0.0

CRAN release: 2023-08-28

Date: 2023-08-28

New Features:

  1. Major version update: we have developed the Shiny UI for the TOmicsVis package. If you install the latest version of TOmicsVis-v2.0.0 or above, you can use the `TOmicsVis::tomicsvis()’function to start the Shiny application locally.

Bugs Fixed:

TOmicsVis 1.2.8

Date: 2023-08-25

New Features:

  1. Create ?TOmicsVis::gene_go_kegg dataset.
  2. Update ?TOmicsVis::chord_plot function.
  3. Create ?TOmicsVis::gene_go_kegg2 dataset.
  4. Update ?TOmicsVis::go_enrich function.
  5. Create ?TOmicsVis::network_data dataset.
  6. Update ?TOmicsVis::network_plot function.
  7. Update ?TOmicsVis::wgcna_pipeline function.
  8. Update ?TOmicsVis::kegg_enrich function.
  9. Update ?TOmicsVis::table_split function.
  10. Update ?TOmicsVis::table_merge function.
  11. Update ?TOmicsVis::table_cross function.

Bugs Fixed:

TOmicsVis 1.2.7

Date: 2023-08-24

New Features:

  1. Create ?TOmicsVis::gene_expression2 dataset.
  2. Update ?TOmicsVis::circos_heatmap function.
  3. Create ?TOmicsVis::degs_stats dataset.
  4. Update ?TOmicsVis::volcano_plot function.
  5. Create ?TOmicsVis::degs_stats2 dataset.
  6. Update ?TOmicsVis::ma_plot function.
  7. Update ?TOmicsVis::heatmap_group function.
  8. Create ?TOmicsVis::gene_expression3 dataset.
  9. Update ?TOmicsVis::trend_plot function.
  10. Update ?TOmicsVis::gene_cluster_trend function.
  11. Update ?TOmicsVis::gene_rank_plot function.
  12. Update ?TOmicsVis::heatmap_cluster function.

Bugs Fixed:

TOmicsVis 1.2.6

Date: 2023-08-23

New Features:

  1. Create data-tables for store demo tables.
  2. Update ?TOmicsVis::dendro_plot function.
  3. Create ?TOmicsVis::traits_sex dataset.
  4. Update ?TOmicsVis::box_plot function.
  5. Update ?TOmicsVis::violin_plot function.
  6. Update ?TOmicsVis::survival_plot function.
  7. Create ?TOmicsVis::paired_degs dataset.
  8. Update ?TOmicsVis::venn_plot function.
  9. Update ?TOmicsVis::flower_plot function.

Bugs Fixed:

TOmicsVis 1.2.5

Date: 2023-08-22

New Features:

  1. Create data-tables for store demo tables.
  2. Create ?TOmicsVis::weight_sex dataset.
  3. Update ?TOmicsVis::quantile_plot function.
  4. Create ?TOmicsVis::gene_expression dataset.
  5. Update ?TOmicsVis::corr_heatmap function.
  6. Create ?TOmicsVis::samples_groups dataset.
  7. Update ?TOmicsVis::pca_plot function.
  8. Update ?TOmicsVis::tsne_plot function.

Bugs Fixed:

TOmicsVis 1.2.4

Date: 2023-07-26

New Features:

Bugs Fixed:

  1. Add new parameters (cluster_run, dend_show, rowname_show) for ?TOmicsVis::circos_heatmap function.

TOmicsVis 1.2.3

CRAN release: 2023-07-20

Date: 2023-07-20

New Features:

Bugs Fixed:

  1. Update R-4.2.2 to R-4.3.1.
  2. Fixed CRAN problems by close go_enrich_tree and kegg_enrich_tree.
  3. Update heatmap_cluster function.
  4. Update pkgdown website: Installation, Tutorials, Courses.

TOmicsVis 1.2.2

Date: 2023-07-18

New Features:

Bugs Fixed:

  1. Fixed ?TOmicsVis::box_plot and ?TOmicsVis::violin_plot by changing wilcox.test to t.test.
  2. Fixed ?TOmicsVis::dendro_plot by adding supperssWarning.
  3. Fixed ?TOmicsVis::tsne_plot by changing aes to aes_string.
  4. Fixed function for avoiding warning messages.
  5. Fixed ?TOmicsVis::go_enrich_bar and ?TOmicsVis::kegg_enrich_bar Count aes.

TOmicsVis 1.2.1

Date: 2023-07-14

New Features:

Bugs Fixed:

  1. Fixed ?TOmicsVis::tsne_plot function.
  2. Change README.Rmd fig.width=10.00, fig.height=6.18.
  3. Update GO and KEGG example datasets.
  4. Fixed GO and KEGG enrichment results.

TOmicsVis 1.2.0

Date: 2023-07-07

New Features:

Bugs Fixed:

  1. Add e1071 to Denps in DESCRIPTION.
  2. Fixed gene_cluster_trend.R, flower_plot.

TOmicsVis 1.1.9

Date: 2023-07-07

New Features:

  1. New ?TOmicsVis::gene_cluster_data plot function.
  2. New ?TOmicsVis::gene_cluster_trend plot function.
  3. New ?TOmicsVis::flower_plot plot function.

Bugs Fixed:

TOmicsVis 1.1.8

CRAN release: 2023-07-06

Date: 2023-07-06

New Features:

Bugs Fixed:

  1. Fixed DESCRIPTION: Title, Description, Authors.
  2. Fixed return and \value: wgcna_pipeline.Rd.
  3. Fixed examples are commented out: circos_heatmap.Rd, wgcna_pipeline.Rd.
  4. Fixed dir.create() to tempdir(): wgcna_pipeline.R.
  5. Fixed seed to a specific number: tsne_plot.R.
  6. Fixed Lengthy examples (> 5 sec):

TOmicsVis 1.1.7

Date: 2023-07-05

New Features:

  1. New ?TOmicsVis::dendro_plot plot function.
  2. New ?TOmicsVis::gene_rank_plot plot function.
  3. New vignettes documents.

Bugs Fixed:

TOmicsVis 1.1.6

Date: 2023-07-03

New Features:

Bugs Fixed:

  1. Fixed test problems from CRAN team.
  2. Update README.rmd and README.md.

TOmicsVis 1.1.5

Date: 2023-07-02

New Features:

  1. New ?TOmicsVis::heatmap_group_data plot function.
  2. New ?TOmicsVis::heatmap_group plot function.

Bugs Fixed:

  1. Fixed import and importFrom problems.

TOmicsVis 1.1.4

Date: 2023-07-01

New Features:

  1. New ?TOmicsVis::network_data plot function.
  2. New ?TOmicsVis::network_plot plot function.
  3. New ?TOmicsVis::wgcna_gene_exp plot function.
  4. New ?TOmicsVis::wgcna_sample_group plot function.
  5. New ?TOmicsVis::wgcna_pipeline plot function.

Bugs Fixed:

  1. None.

TOmicsVis 1.1.3

Date: 2023-06-30

New Features:

  1. New ?TOmicsVis::kegg_enrich plot function.
  2. New ?TOmicsVis::kegg_enrich_bar plot function.
  3. New ?TOmicsVis::kegg_enrich_dot plot function.
  4. New ?TOmicsVis::kegg_enrich_tree plot function.
  5. New ?TOmicsVis::kegg_enrich_net plot function.

Bugs Fixed:

  1. None.

TOmicsVis 1.1.2

Date: 2023-06-30

New Features:

  1. New ?TOmicsVis::go_enrich_bar plot function.
  2. New ?TOmicsVis::go_enrich_dot plot function.
  3. New ?TOmicsVis::go_enrich_tree plot function.
  4. New ?TOmicsVis::go_enrich_net plot function.

Bugs Fixed:

  1. None.

TOmicsVis 1.1.1

Date: 2023-06-30

New Features:

  1. New ?TOmicsVis::go_anno example dataset.
  2. New ?TOmicsVis::go_deg_fc plot function.
  3. New ?TOmicsVis::go_enrich plot function.
  4. New ?TOmicsVis::go_enrich_stat plot function.

Bugs Fixed:

  1. None.

TOmicsVis 1.1.0

Date: 2023-06-28

New Features:

  1. New ?TOmicsVis::table_cross_data1 example dataset.
  2. New ?TOmicsVis::table_cross_data2 plot function.
  3. New ?TOmicsVis::table_cross plot function.

Bugs Fixed:

  1. None.

TOmicsVis 1.0.9

Date: 2023-06-27

New Features:

  1. New ?TOmicsVis::table_merge_data example dataset.
  2. New ?TOmicsVis::table_merge plot function.
  3. New ?TOmicsVis::table_filter_data example dataset.
  4. New ?TOmicsVis::table_filter plot function.

Bugs Fixed:

  1. None.

TOmicsVis 1.0.8

Date: 2023-06-26

New Features:

  1. New ?TOmicsVis::survival_data example dataset.
  2. New ?TOmicsVis::survival_plot plot function.
  3. New ?TOmicsVis::tsne_data example dataset.
  4. New ?TOmicsVis::tsne_plot plot function.

Bugs Fixed:

  1. None.

TOmicsVis 1.0.7

Date: 2023-06-26

New Features:

  1. New ?TOmicsVis::trend_data example dataset.
  2. New ?TOmicsVis::trend_plot plot function.
  3. New ?TOmicsVis::table_split_data example dataset.
  4. New ?TOmicsVis::table_split plot function.

Bugs Fixed:

  1. Fixed _pkgdown.yml categories and functions.

TOmicsVis 1.0.6

Date: 2023-06-25

New Features:

  1. New ?TOmicsVis::deg_data example dataset.
  2. New ?TOmicsVis::volcano_plot plot function.
  3. New ?TOmicsVis::deg_data2 example dataset.
  4. New ?TOmicsVis::ma_plot plot function.

Bugs Fixed:

  1. None.

TOmicsVis 1.0.5

Date: 2023-06-24

New Features:

  1. New ?TOmicsVis::chord_data example dataset.
  2. New ?TOmicsVis::chord_plot plot function.
  3. New ?TOmicsVis::circos_heatmap_data example dataset.
  4. New ?TOmicsVis::circos_heatmap plot function.

Bugs Fixed:

  1. Set function invisible().

TOmicsVis 1.0.4

Date: 2023-06-23

New Features:

  1. New ?TOmicsVis::quantile_data example dataset.
  2. New ?TOmicsVis::quantile_plot plot function.
  3. New ?TOmicsVis::venn_data example dataset.
  4. New ?TOmicsVis::venn_plot plot function.

Bugs Fixed:

  1. None.

TOmicsVis 1.0.3

Date: 2023-06-22

New Features:

  1. New ?TOmicsVis::box_data example datasets.
  2. New ?TOmicsVis::box_plot plot function.
  3. New ?TOmicsVis::violin_plot plot function.

Bugs Fixed:

  1. Fixed _pkgdown.yml theme configure.

TOmicsVis 1.0.2

Date: 2023-06-21

New Features:

  1. New ?TOmicsVis::pca_sample_gene and ?TOmicsVis::pca_group_sample example datasets.
  2. New ?TOmicsVis::pca_plot plot function.

Bugs Fixed:

  1. Fixed _pkgdown.yml configure reference ggplot2: https://github.com/tidyverse/ggplot2/blob/main/README.Rmd.

TOmicsVis 1.0.1

Date: 2023-06-20

New Features:

  1. Open source code of TOmicsVis to github: https://github.com/benben-miao/TOmicsVis/.
  2. Build pkgdown website: https://benben-miao.github.io/TOmicsVis/ for TOmicsVis package.

Bugs Fixed:

  1. Fixed DESCRIPTION import parameters
  2. Fixed _pkgdown.yml configure file using Visual Studio Code.

TOmicsVis 1.0.0

Date: 2023-06-20

New Features:

  1. Create TOmicsVis package and complete the DESCRIPTION file.
  2. New ?TOmicsVis::gene_exp example data and ?TOmicsVis::corr_heatmap function.

Bugs Fixed:

None