Package: GPflexViz 1.0.0

GPflexViz: Graphical Visualizations Related to Genomic Prediction

Provides flexible tools for the visualization of genomic data. Supports interactive and static plots tailored for presentations and publications, with customizable features like colors, themes, and annotations to align with specific analytical and presentation goals.

Authors:Dovini Jayasinghe [aut, cre, cph], Hong Lee [aut, cph]

GPflexViz_1.0.0.tar.gz
GPflexViz_1.0.0.zip(r-4.7-any)GPflexViz_1.0.0.zip(r-4.6-any)GPflexViz_1.0.0.zip(r-4.5-any)
GPflexViz_1.0.0.tgz(r-4.6-any)GPflexViz_1.0.0.tgz(r-4.5-any)
GPflexViz_1.0.0.tar.gz(r-4.7-any)GPflexViz_1.0.0.tar.gz(r-4.6-any)
GPflexViz_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
GPflexViz/json (API)

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

Bug tracker:https://github.com/dovinij/gpflexviz/issues

Datasets:
  • example_data1 - Gwas_data with all chromosome information This contains Single nucleotide polymorphism (SNP) information.
  • example_data10 - Regression_data This contains estimation and p value data from a/the regression summary output/s.
  • example_data11 - CI_data This contains individual level data for constructing confidence intervals
  • example_data2 - Gwas_data with partial chromosome information This contains Single nucleotide polymorphism (SNP) information.
  • example_data3 - Accuracy_data with full information This contains prediction accuracy related information.
  • example_data4 - Accuracy_data with partial information This contains prediction accuracy related information.
  • example_data5 - Comparison_data This contains prediction accuracy related information for model comparison.
  • example_data6 - Accuracy_diff_data This contains prediction accuracy related information for detailed model comparison (2 methods at a time).
  • example_data7 - Ld_data This contains Linkage Disequilibrium (LD) related data (e.g. pair-wise variant correlation squared).
  • example_data8 - Distribution_data This contains data for consruction of histograms/density plots, with at least 1 column.
  • example_data9 - Correlation_matrix A 20x20 symmetric matrix containing correlation coefficients between various variables (e.g. varients, individuals).

On CRAN:

Conda:

3.18 score 3 stars 1 scripts 341 downloads 11 exports 74 dependencies

Last updated from:ffd96511e0. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK168
source / vignettesOK197
linux-releaseOK161
macos-releaseOK186
macos-oldrelOK230
windows-develOK113
windows-releaseOK123
windows-oldrelOK139
wasm-releaseOK120

Exports:flex_accuracyflex_accuracy_diffflex_accuracy_diff2flex_boxplotflex_correlation_plotflex_distributionflex_intervalflex_LD_decayflex_manhattanflex_qqplotflex_regression_summary

Dependencies:askpassbase64encbslibcachemclicowplotcpp11crosstalkcurldata.tabledigestdplyrevaluatefarverfastmapfontawesomefsgenericsggforceggplot2gluegridExtragtablehighrhtmltoolshtmlwidgetshttrisobandjquerylibjsonliteknitrlabelinglaterlazyevallifecyclemagrittrMASSmemoisemimenortestopensslotelpillarpkgconfigplotlyplyrpolyclippromisespurrrR6rappdirsRColorBrewerRcppreshape2rlangrmarkdownS7sassscalesstringistringrsyssystemfontstibbletidyrtidyselecttinytextweenrutf8vctrsviridisLitewithrxfunyaml

Readme and manuals

Help Manual

Help pageTopics
gwas_data with all chromosome information This contains Single nucleotide polymorphism (SNP) information.example_data1
regression_data This contains estimation and p value data from a/the regression summary output/s.example_data10
CI_data This contains individual level data for constructing confidence intervalsexample_data11
gwas_data with partial chromosome information This contains Single nucleotide polymorphism (SNP) information.example_data2
accuracy_data with full information This contains prediction accuracy related information.example_data3
accuracy_data with partial information This contains prediction accuracy related information.example_data4
comparison_data This contains prediction accuracy related information for model comparison.example_data5
accuracy_diff_data This contains prediction accuracy related information for detailed model comparison (2 methods at a time).example_data6
ld_data This contains Linkage Disequilibrium (LD) related data (e.g. pair-wise variant correlation squared).example_data7
distribution_data This contains data for consruction of histograms/density plots, with at least 1 column.example_data8
correlation_matrix A 20x20 symmetric matrix containing correlation coefficients between various variables (e.g. varients, individuals).example_data9
flex_accuracy functionflex_accuracy
flex_accuracy_diff functionflex_accuracy_diff
flex_accuracy_diff2 functionflex_accuracy_diff2
flex_boxplot functionflex_boxplot
flex_correlation_plot functionflex_correlation_plot
flex_distribution functionflex_distribution
flex_interval functionflex_interval
flex_LD_decay functionflex_LD_decay
flex_manhattan functionflex_manhattan
flex_qqplot functionflex_qqplot
flex_regression_summary functionflex_regression_summary