Package: hidecan 1.1.0.9000

Olivia Angelin-Bonnet

hidecan: Create HIDECAN Plots for Visualising Genome-Wide Association Studies and Differential Expression Results

Generates HIDECAN plots that summarise and combine the results of genome-wide association studies (GWAS) and transcriptomics differential expression analyses (DE), along with manually curated candidate genes of interest. The HIDECAN plot is presented in: Angelin-Bonnet, O., Vignes, M., Biggs, P. J., Baldwin, S., & Thomson, S. (2023). Visual integration of GWAS and differential expression results with the hidecan R package. bioRxiv, 2023-03.

Authors:Olivia Angelin-Bonnet [aut, cre]

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hidecan/json (API)
NEWS

# Install 'hidecan' in R:
install.packages('hidecan', repos = c('https://plantandfoodresearch.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/plantandfoodresearch/hidecan/issues

On CRAN:

17 exports 4 stars 1.47 score 70 dependencies 1 dependents 14 scripts 243 downloads

Last updated 0 hours agofrom:ee0d6a100b. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 18 2024
R-4.5-winOKSep 18 2024
R-4.5-linuxOKSep 18 2024
R-4.4-winOKSep 18 2024
R-4.4-macOKSep 18 2024
R-4.3-winOKSep 18 2024
R-4.3-macOKSep 18 2024

Exports:.compute_chrom_length_genes.compute_chrom_length_markersapply_thresholdCAN_datacombine_chrom_lengthcompute_chrom_lengthcreate_hidecan_plotCUSTOM_dataDE_dataget_example_dataGWAS_dataGWAS_data_from_gwaspolyhidecan_aeshidecan_plothidecan_plot_from_gwaspolymanhattan_plotrun_hidecan_shiny

Dependencies:base64encbitbit64bslibcachemclicolorspacecommonmarkcpp11crayondigestdplyrfansifarverfastmapfontawesomefsgenericsggnewscaleggplot2ggrepelgluegridExtragtablehmshtmltoolshttpuvisobandjquerylibjsonlitelabelinglaterlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmepillarpkgconfigprettyunitsprogresspromisespurrrR6rappdirsRColorBrewerRcpprlangsassscalesshinysourcetoolsstringistringrtibbletidyrtidyselecttzdbutf8vctrsviridisviridisLitevroomwithrxtable

hidecan

Rendered fromhidecan.Rmdusingknitr::rmarkdownon Sep 18 2024.

Last update: 2024-09-18
Started: 2022-12-08

Creating a HIDECAN plot step by step

Rendered fromhidecan-step-by-step.Rmdusingknitr::rmarkdownon Sep 18 2024.

Last update: 2023-02-15
Started: 2022-12-08

Readme and manuals

Help Manual

Help pageTopics
Add data type to HIDECAN plot.add_data_type
Check chromosome limits.check_chrom_limits
Check chromosomes to plot.check_chroms
Checks whether some columns are present in a tibble.check_cols
Computes chromosomes' length for a tibble of genes.compute_chrom_length_genes
Computes chromosomes' length for a tibble of markers.compute_chrom_length_markers
Returns either "aes_type" attribute or object class.get_aes_type
Computes plot aesthetics.get_plot_aes
Filters GWAS or DE results based on a thresholdapply_threshold apply_threshold.CAN_data apply_threshold.CUSTOM_data apply_threshold.default apply_threshold.DE_data apply_threshold.GWAS_data
Creates a 'CAN_data' objectCAN_data
Computes chromosomes' length from listcombine_chrom_length
Computes chromosomes' lengthcompute_chrom_length compute_chrom_length.CAN_data compute_chrom_length.CUSTOM_data compute_chrom_length.DE_data compute_chrom_length.GWAS_data
Creates a HIDECAN plotcreate_hidecan_plot
Creates a 'CUSTOM_data' objectCUSTOM_data
Creates a 'DE_data' objectDE_data
Example datasetget_example_data
Creates a 'GWAS_data' objectGWAS_data
Extracts information from GWASpoly outputGWAS_data_from_gwaspoly
Default aesthetics for HIDECAN plothidecan_aes
Wrapper to create a HIDECAN plothidecan_plot
Creates a HIDECAN plot from GWASpoly outputhidecan_plot_from_gwaspoly
Creates a Manhattan plotmanhattan_plot
'CAN_data' constructornew_CAN_data
'CUSTOM_data' constructornew_CUSTOM_data
'DE_data' constructornew_DE_data
'GWAS_data' constructornew_GWAS_data
Launches the HIDECAN shiny apprun_hidecan_shiny
Checks validity of input for 'CAN_data' constructorvalidate_CAN_data
Checks validity of input for 'CUSTOM_data' constructorvalidate_CUSTOM_data
Checks validity of input for 'DE_data' constructorvalidate_DE_data
Checks validity of input for 'GWAS_data' constructorvalidate_GWAS_data