qtlcharts: Interactive Graphics for QTL Experiments
Version 0.7-8

Web-based interactive charts (using D3.js) for the analysis of experimental crosses to identify genetic loci (quantitative trait loci, QTL) contributing to variation in quantitative traits.

AuthorKarl W Broman [aut, cre], Michael Bostock [ctb, cph] (d3.js library in htmlwidgets/lib, http://d3js.org), Justin Palmer [ctb, cph] (d3.tip library in htmlwidgets/lib, https://github.com/caged/d3-tip), Cynthia Brewer [cph] (ColorBrewer library in htmlwidgets/lib, http://colorbrewer2.org), Mark Harrower [cph] (ColorBrewer library in htmlwidgets/lib, http://colorbrewer2.org), The Pennsylvania State University [cph] (ColorBrewer library in htmlwidgets/lib, http://colorbrewer2.org), jQuery Foundation [cph] (jQuery library in htmlwidgets/lib, http://jquery.com), jQuery contributors [ctb] (jQuery library in htmlwidgets/lib; see https://github.com/jquery/jquery/blob/master/AUTHORS.txt), jQuery UI contributors [ctb] (jQuery UI library in htmlwidgets/lib; see http://jqueryui.com/about)
Date of publication2016-06-28 23:43:10
MaintainerKarl W Broman <kbroman@biostat.wisc.edu>
LicenseGPL-3 | file LICENSE
Version0.7-8
URL http://kbroman.org/qtlcharts
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("qtlcharts")

Getting started

Package overview

Popular man pages

iboxplot: Modern boxplot linked to underlying histrograms
idotplot: Interactive phenotype x genotype plot
iheatmap: Interactive heat map
iplotCorr: Image of correlation matrix with linked scatterplot
iplotScanone: Interactive LOD curve
qtlcharts-package: R/qtlcharts: Interactive charts for QTL data
qtlcharts-shiny: Shiny bindings for R/qtlcharts widgets
See all...

All man pages Function index File listing

Man pages

cbindQTLeffects: Combine multiple runs of estQTLeffects
estQTLeffects: Calculate QTL effects at each position across the genome
geneExpr: Anonymized gene expression data
grav: Arabidopsis QTL data on gravitropism
iboxplot: Modern boxplot linked to underlying histrograms
idotplot: Interactive phenotype x genotype plot
iheatmap: Interactive heat map
iplot: Interactive scatterplot
iplotCorr: Image of correlation matrix with linked scatterplot
iplotCurves: Plot of a bunch of curves, linked to points in scatterplots
iplotMap: Interactive genetic map plot
iplotMScanone: Interactive LOD curve
iplotPXG: Interactive phenotype x genotype plot
iplotRF: Interactive plot of recombination fractions
iplotScanone: Interactive LOD curve
iplotScantwo: Interactive plot of 2d genome scan
itriplot: Interactive plot of trinomial probabilities
qtlcharts-package: R/qtlcharts: Interactive charts for QTL data
qtlcharts-shiny: Shiny bindings for R/qtlcharts widgets
qtlchartsversion: print the installed version of R/qtlcharts
scat2scat: Scatterplot driving another scatterplot
setScreenSize: Set default maximum screen size

Functions

add2chartOpts Source code
calcSignedLOD Source code
cbindQTLeffects Man page Source code
convert2effects Source code
convert4crosstab Source code
convert4iboxplot Source code
convert4iplotcorr Source code
convert_effects Source code
convert_map Source code
convert_pxg Source code
convert_scanone Source code
cross4iplotScantwo Source code
data4iplotRF Source code
data4iplotScantwo Source code
estQTLeffects Man page Source code
extractPheno Source code
geneExpr Man page
getImputedGenotypes Source code
getPhename Source code
getPlotSize Source code
getScreenSize Source code
get_indID Source code
get_lodv1 Source code
grabarg Source code
grav Man page
group2numeric Source code
iboxplot Man page Source code
iboxplot_output Man page Source code
iboxplot_render Man page Source code
idotplot Man page Source code
idotplot_output Man page Source code
idotplot_render Man page Source code
iheatmap Man page Source code
iheatmap_output Man page Source code
iheatmap_render Man page Source code
iplot Man page Source code
iplotCorr Man page Source code
iplotCorr_output Man page Source code
iplotCorr_render Man page Source code
iplotCurves Man page Source code
iplotCurves_output Man page Source code
iplotCurves_render Man page Source code
iplotMScanone Man page Source code
iplotMScanone_output Man page Source code
iplotMScanone_render Man page Source code
iplotMap Man page Source code
iplotMap_output Man page Source code
iplotMap_render Man page Source code
iplotPXG Man page Source code
iplotRF Man page Source code
iplotRF_output Man page Source code
iplotRF_render Man page Source code
iplotScanone Man page Source code
iplotScanone_output Man page Source code
iplotScanone_render Man page Source code
iplotScantwo Man page Source code
iplotScantwo_output Man page Source code
iplotScantwo_render Man page Source code
iplot_output Man page Source code
iplot_render Man page Source code
is_equally_spaced Source code
itriplot Man page Source code
itriplot_output Man page Source code
itriplot_render Man page Source code
qtlcharts Man page
qtlcharts-package Man page
qtlcharts-shiny Man page
qtlchartsversion Man page Source code
revisePmarNames Source code
scat2scat Man page Source code
scat2scat_output Man page Source code
scat2scat_render Man page Source code
selectMatrixColumns Source code
setScreenSize Man page Source code

Files

inst
inst/htmlwidgets
inst/htmlwidgets/iboxplot.yaml
inst/htmlwidgets/iplotScantwo.js
inst/htmlwidgets/scat2scat.js
inst/htmlwidgets/iplotCorr.coffee
inst/htmlwidgets/itriplot.coffee
inst/htmlwidgets/iplotScanone.js
inst/htmlwidgets/lib
inst/htmlwidgets/lib/d3-tip
inst/htmlwidgets/lib/d3-tip/index-min.js
inst/htmlwidgets/lib/d3-tip/ReadMe.md
inst/htmlwidgets/lib/d3-tip/LICENSE
inst/htmlwidgets/lib/jquery-ui
inst/htmlwidgets/lib/jquery-ui/LICENSE.txt
inst/htmlwidgets/lib/jquery-ui/jquery-ui.min.js
inst/htmlwidgets/lib/jquery-ui/themes
inst/htmlwidgets/lib/jquery-ui/themes/smoothness
inst/htmlwidgets/lib/jquery-ui/themes/smoothness/theme.css
inst/htmlwidgets/lib/jquery-ui/themes/smoothness/jquery-ui.min.css
inst/htmlwidgets/lib/jquery-ui/themes/smoothness/images
inst/htmlwidgets/lib/jquery-ui/themes/smoothness/images/ui-icons_222222_256x240.png
inst/htmlwidgets/lib/jquery-ui/themes/smoothness/images/ui-bg_flat_75_ffffff_40x100.png
inst/htmlwidgets/lib/jquery-ui/themes/smoothness/images/ui-bg_glass_75_dadada_1x400.png
inst/htmlwidgets/lib/jquery-ui/themes/smoothness/images/animated-overlay.gif
inst/htmlwidgets/lib/jquery-ui/themes/smoothness/images/ui-icons_2e83ff_256x240.png
inst/htmlwidgets/lib/jquery-ui/themes/smoothness/images/ui-longname.png
inst/htmlwidgets/lib/jquery-ui/themes/smoothness/images/ui-bg_glass_65_ffffff_1x400.png
inst/htmlwidgets/lib/jquery-ui/themes/smoothness/images/ui-bg_flat_0_aaaaaa_40x100.png
inst/htmlwidgets/lib/jquery-ui/themes/smoothness/images/ui-bg_glass_95_fef1ec_1x400.png
inst/htmlwidgets/lib/jquery-ui/themes/smoothness/images/ui-icons_cd0a0a_256x240.png
inst/htmlwidgets/lib/jquery-ui/themes/smoothness/images/ui-bg_glass_75_e6e6e6_1x400.png
inst/htmlwidgets/lib/jquery-ui/themes/smoothness/images/ui-icons_888888_256x240.png
inst/htmlwidgets/lib/jquery-ui/themes/smoothness/images/ui-icons_454545_256x240.png
inst/htmlwidgets/lib/jquery-ui/themes/smoothness/images/ui-bg_glass_55_fbf9ee_1x400.png
inst/htmlwidgets/lib/jquery-ui/themes/smoothness/jquery-ui.css
inst/htmlwidgets/lib/jquery
inst/htmlwidgets/lib/jquery/MIT-LICENSE.txt
inst/htmlwidgets/lib/jquery/dist
inst/htmlwidgets/lib/jquery/dist/jquery.min.js
inst/htmlwidgets/lib/d3panels
inst/htmlwidgets/lib/d3panels/License.md
inst/htmlwidgets/lib/d3panels/ReadMe.md
inst/htmlwidgets/lib/d3panels/d3panels.min.css
inst/htmlwidgets/lib/d3panels/d3panels.min.js
inst/htmlwidgets/lib/colorbrewer
inst/htmlwidgets/lib/colorbrewer/ReadMe.md
inst/htmlwidgets/lib/colorbrewer/colorbrewer.css
inst/htmlwidgets/lib/colorbrewer/colorbrewer.js
inst/htmlwidgets/lib/colorbrewer/LICENSE
inst/htmlwidgets/lib/qtlcharts
inst/htmlwidgets/lib/qtlcharts/iplotScantwo.js
inst/htmlwidgets/lib/qtlcharts/scat2scat.js
inst/htmlwidgets/lib/qtlcharts/iplotScanone_pxg.js
inst/htmlwidgets/lib/qtlcharts/iplotMScanone_eff.coffee
inst/htmlwidgets/lib/qtlcharts/iplotScanone_noeff.coffee
inst/htmlwidgets/lib/qtlcharts/iplotCorr.coffee
inst/htmlwidgets/lib/qtlcharts/itriplot.coffee
inst/htmlwidgets/lib/qtlcharts/charts.css
inst/htmlwidgets/lib/qtlcharts/iplotMScanone_noeff.js
inst/htmlwidgets/lib/qtlcharts/iboxplot.coffee
inst/htmlwidgets/lib/qtlcharts/iplotMap.coffee
inst/htmlwidgets/lib/qtlcharts/idotplot.js
inst/htmlwidgets/lib/qtlcharts/iplot.js
inst/htmlwidgets/lib/qtlcharts/iplotMap.js
inst/htmlwidgets/lib/qtlcharts/iplot.coffee
inst/htmlwidgets/lib/qtlcharts/iplotScanone_noeff.js
inst/htmlwidgets/lib/qtlcharts/iheatmap.js
inst/htmlwidgets/lib/qtlcharts/iplotCorr.js
inst/htmlwidgets/lib/qtlcharts/iplotRF.coffee
inst/htmlwidgets/lib/qtlcharts/iplotCurves.coffee
inst/htmlwidgets/lib/qtlcharts/iplotCorr_noscat.js
inst/htmlwidgets/lib/qtlcharts/iplotRF.js
inst/htmlwidgets/lib/qtlcharts/iplotMScanone_eff.js
inst/htmlwidgets/lib/qtlcharts/iboxplot.js
inst/htmlwidgets/lib/qtlcharts/itriplot.js
inst/htmlwidgets/lib/qtlcharts/scat2scat.coffee
inst/htmlwidgets/lib/qtlcharts/iplotScanone_ci.coffee
inst/htmlwidgets/lib/qtlcharts/iplotScanone_ci.js
inst/htmlwidgets/lib/qtlcharts/iplotCurves.js
inst/htmlwidgets/lib/qtlcharts/iplotScantwo.coffee
inst/htmlwidgets/lib/qtlcharts/iplotCorr_noscat.coffee
inst/htmlwidgets/lib/qtlcharts/idotplot.coffee
inst/htmlwidgets/lib/qtlcharts/iheatmap.coffee
inst/htmlwidgets/lib/qtlcharts/iplotMScanone_noeff.coffee
inst/htmlwidgets/lib/qtlcharts/iplotScanone_pxg.coffee
inst/htmlwidgets/lib/d3
inst/htmlwidgets/lib/d3/ReadMe.md
inst/htmlwidgets/lib/d3/d3.min.js
inst/htmlwidgets/lib/d3/LICENSE
inst/htmlwidgets/iplotCorr.yaml
inst/htmlwidgets/iboxplot.coffee
inst/htmlwidgets/iplotMap.coffee
inst/htmlwidgets/iplotScantwo.yaml
inst/htmlwidgets/idotplot.js
inst/htmlwidgets/iplotRF.yaml
inst/htmlwidgets/iplot.js
inst/htmlwidgets/iplotMap.yaml
inst/htmlwidgets/iplotMScanone.js
inst/htmlwidgets/iplotMScanone.coffee
inst/htmlwidgets/iplotMap.js
inst/htmlwidgets/iplot.coffee
inst/htmlwidgets/iheatmap.js
inst/htmlwidgets/iplotCorr.js
inst/htmlwidgets/iplotScanone.yaml
inst/htmlwidgets/iplotScanone.coffee
inst/htmlwidgets/iplotRF.coffee
inst/htmlwidgets/iplotCurves.coffee
inst/htmlwidgets/scat2scat.yaml
inst/htmlwidgets/iplotRF.js
inst/htmlwidgets/iboxplot.js
inst/htmlwidgets/itriplot.js
inst/htmlwidgets/scat2scat.coffee
inst/htmlwidgets/itriplot.yaml
inst/htmlwidgets/iplotCurves.yaml
inst/htmlwidgets/iplotCurves.js
inst/htmlwidgets/iplotScantwo.coffee
inst/htmlwidgets/idotplot.coffee
inst/htmlwidgets/iheatmap.coffee
inst/htmlwidgets/iheatmap.yaml
inst/htmlwidgets/idotplot.yaml
inst/htmlwidgets/iplotMScanone.yaml
inst/htmlwidgets/iplot.yaml
inst/CITATION
inst/ToDo.md
inst/NEWS.md
inst/ReadMe.md
inst/LICENSE
tests
tests/Rmdtest.R
tests/Rmdtest
tests/Rmdtest/iplotRF.Rmd
tests/Rmdtest/itriplot.Rmd
tests/Rmdtest/iplotCorr.Rmd
tests/Rmdtest/iplotScanone.Rmd
tests/Rmdtest/iheatmap.Rmd
tests/Rmdtest/iplotMap.Rmd
tests/Rmdtest/scat2scat.Rmd
tests/Rmdtest/iplotMScanone.Rmd
tests/Rmdtest/iplot.Rmd
tests/Rmdtest/iplotScantwo.Rmd
tests/Rmdtest/iplotCurves_justcurves.Rmd
tests/Rmdtest/iplotCurves.Rmd
tests/Rmdtest/iplotPXG.Rmd
tests/Rmdtest/Rmdtest.Rmd
tests/Rmdtest/iboxplot.Rmd
tests/Rmdtest/idotplot.Rmd
tests/htmltest
tests/htmltest/iboxplot.R
tests/htmltest/iplotMap.R
tests/htmltest/iplot.R
tests/htmltest/idotplot.R
tests/htmltest/scat2scat.R
tests/htmltest/iheatmap.R
tests/htmltest/iplotScantwo.R
tests/htmltest/itriplot.R
tests/htmltest/iplotPXG.R
tests/htmltest/iplotScanone.R
tests/htmltest/iplotCurves_justcurves.R
tests/htmltest/iplotCorr.R
tests/htmltest/iplotCurves.R
tests/htmltest/iplotMScanone.R
tests/htmltest/iplotRF.R
tests/htmltest.R
tests/testthat.R
tests/testthat
tests/testthat/test-chartopts.R
tests/testthat/test-group.R
tests/testthat/test-qtleffects.R
tests/testthat/test-util.R
NAMESPACE
data
data/geneExpr.rda
data/grav.rda
R
R/iboxplot.R
R/convert_pxg.R
R/iplotMap.R
R/convert_scanone.R
R/qtlcharts.R
R/grav-data.R
R/iplot.R
R/idotplot.R
R/geneExpr-data.R
R/scat2scat.R
R/convert4crosstab.R
R/convert4iplotcorr.R
R/estQTLeffects.R
R/iheatmap.R
R/convert4iboxplot.R
R/iplotScantwo.R
R/chartOpts.R
R/itriplot.R
R/convert_map.R
R/util.R
R/iplotPXG.R
R/iplotScanone.R
R/setScreenSize.R
R/iplotCorr.R
R/qtlchartsversion.R
R/iplotCurves.R
R/iplotMScanone.R
R/iplotRF.R
MD5
DESCRIPTION
configure
man
man/qtlchartsversion.Rd
man/iplotMap.Rd
man/iplot.Rd
man/itriplot.Rd
man/iplotScantwo.Rd
man/iplotMScanone.Rd
man/geneExpr.Rd
man/iplotPXG.Rd
man/cbindQTLeffects.Rd
man/iplotRF.Rd
man/iboxplot.Rd
man/estQTLeffects.Rd
man/grav.Rd
man/iplotCurves.Rd
man/setScreenSize.Rd
man/idotplot.Rd
man/scat2scat.Rd
man/iplotScanone.Rd
man/iplotCorr.Rd
man/qtlcharts-package.Rd
man/qtlcharts-shiny.Rd
man/iheatmap.Rd
configure.win
LICENSE
qtlcharts documentation built on May 20, 2017, 1:05 a.m.

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