From 0565b2b33b1e23b1d5cdf0e4c90eb33a06663173 Mon Sep 17 00:00:00 2001 From: raivokolde Date: Tue, 5 Jan 2016 11:33:40 -0500 Subject: [PATCH] Added citation --- NAMESPACE | 2 +- R/GOsummaries.R | 4 ++-- inst/CITATION | 18 +++++++++++++++++- man/GOsummaries-package.Rd | 3 ++- man/add_expression.gosummaries.Rd | 3 ++- man/add_to_slot.gosummaries.Rd | 3 ++- man/customize.Rd | 3 ++- man/gosummaries.MArrayLM.Rd | 3 ++- man/gosummaries.Rd | 3 ++- man/gosummaries.kmeans.Rd | 3 ++- man/gosummaries.matrix.Rd | 3 ++- man/gosummaries.prcomp.Rd | 3 ++- man/metabolomic_example.Rd | 3 ++- man/metagenomic_example.Rd | 3 ++- man/panel_boxplot.Rd | 3 ++- man/plot.gosummaries.Rd | 3 ++- man/plotWordcloud.Rd | 3 ++- man/tissue_example.Rd | 3 ++- 18 files changed, 50 insertions(+), 19 deletions(-) diff --git a/NAMESPACE b/NAMESPACE index 17a15d6..1d79d53 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,4 +1,4 @@ -# Generated by roxygen2 (4.0.2): do not edit by hand +# Generated by roxygen2 (4.1.1): do not edit by hand S3method("[",gosummaries) S3method(gosummaries,MArrayLM) diff --git a/R/GOsummaries.R b/R/GOsummaries.R index 56a97c8..68e0ed2 100644 --- a/R/GOsummaries.R +++ b/R/GOsummaries.R @@ -1343,12 +1343,12 @@ panel_violin_box_classes = function(data, fontsize = 10, par){ ## Panel functions for pca data panel_histogram = function(data, fontsize = 10, par){ if(!is.null(par$classes)){ - p = ggplot2::qplot(data$x, geom = "bar", fill = data[, par$classes], + p = ggplot2::qplot(data$x, geom = "histogram", fill = data[, par$classes], binwidth = (max(data$x) - min(data$x)) / 20, colour = I("grey70")) } else{ - p = ggplot2::qplot(data$x, geom = "bar", + p = ggplot2::qplot(data$x, geom = "histogram", binwidth = (max(data$x) - min(data$x)) / 20, data = data) } diff --git a/inst/CITATION b/inst/CITATION index 44aa083..b005573 100644 --- a/inst/CITATION +++ b/inst/CITATION @@ -1 +1,17 @@ -citation(auto = meta) \ No newline at end of file +citHeader("To cite GOsummaries in publications use:") + +citEntry(entry = "Article", + title = "GOsummaries: an R Package for Visual Functional Annotation of Experimental Data", + author = personList(as.person("Raivo Kolde"), + as.person("Jaak Vilo")), + journal = "F1000Research", + year = "2015", + volume = "4", + url = "http://f1000research.com/articles/4-574/v1", + + textVersion = + paste("Raivo Kolde, Jaak Vilo (2015).", + "GOsummaries: an R Package for Visual Functional Annotation of Experimental Data.", + "F1000Research.", + "URL http://f1000research.com/articles/4-574/v1.") +) diff --git a/man/GOsummaries-package.Rd b/man/GOsummaries-package.Rd index dae153b..4246002 100644 --- a/man/GOsummaries-package.Rd +++ b/man/GOsummaries-package.Rd @@ -1,4 +1,5 @@ -% Generated by roxygen2 (4.0.2): do not edit by hand +% Generated by roxygen2 (4.1.1): do not edit by hand +% Please edit documentation in R/GOsummaries-package.R \docType{package} \name{GOsummaries-package} \alias{GOsummaries} diff --git a/man/add_expression.gosummaries.Rd b/man/add_expression.gosummaries.Rd index b0cb816..97c9257 100644 --- a/man/add_expression.gosummaries.Rd +++ b/man/add_expression.gosummaries.Rd @@ -1,4 +1,5 @@ -% Generated by roxygen2 (4.0.2): do not edit by hand +% Generated by roxygen2 (4.1.1): do not edit by hand +% Please edit documentation in R/GOsummaries.R \name{add_expression.gosummaries} \alias{add_expression.gosummaries} \title{Add expression data to gosummaries object} diff --git a/man/add_to_slot.gosummaries.Rd b/man/add_to_slot.gosummaries.Rd index 4e64503..a293d6d 100644 --- a/man/add_to_slot.gosummaries.Rd +++ b/man/add_to_slot.gosummaries.Rd @@ -1,4 +1,5 @@ -% Generated by roxygen2 (4.0.2): do not edit by hand +% Generated by roxygen2 (4.1.1): do not edit by hand +% Please edit documentation in R/GOsummaries.R \name{is.gosummaries} \alias{[.gosummaries} \alias{add_to_slot.gosummaries} diff --git a/man/customize.Rd b/man/customize.Rd index acf830d..10dcc58 100644 --- a/man/customize.Rd +++ b/man/customize.Rd @@ -1,4 +1,5 @@ -% Generated by roxygen2 (4.0.2): do not edit by hand +% Generated by roxygen2 (4.1.1): do not edit by hand +% Please edit documentation in R/GOsummaries.R \name{customize} \alias{customize} \title{Customization function for panel} diff --git a/man/gosummaries.MArrayLM.Rd b/man/gosummaries.MArrayLM.Rd index 1c06886..a9e3ee7 100644 --- a/man/gosummaries.MArrayLM.Rd +++ b/man/gosummaries.MArrayLM.Rd @@ -1,4 +1,5 @@ -% Generated by roxygen2 (4.0.2): do not edit by hand +% Generated by roxygen2 (4.1.1): do not edit by hand +% Please edit documentation in R/GOsummaries.R \name{gosummaries.MArrayLM} \alias{gosummaries.MArrayLM} \title{Prepare gosummaries object based on limma results} diff --git a/man/gosummaries.Rd b/man/gosummaries.Rd index 7f614ea..569db15 100644 --- a/man/gosummaries.Rd +++ b/man/gosummaries.Rd @@ -1,4 +1,5 @@ -% Generated by roxygen2 (4.0.2): do not edit by hand +% Generated by roxygen2 (4.1.1): do not edit by hand +% Please edit documentation in R/GOsummaries.R \name{gosummaries} \alias{gosummaries} \alias{gosummaries.default} diff --git a/man/gosummaries.kmeans.Rd b/man/gosummaries.kmeans.Rd index 7c6b487..12f5cef 100644 --- a/man/gosummaries.kmeans.Rd +++ b/man/gosummaries.kmeans.Rd @@ -1,4 +1,5 @@ -% Generated by roxygen2 (4.0.2): do not edit by hand +% Generated by roxygen2 (4.1.1): do not edit by hand +% Please edit documentation in R/GOsummaries.R \name{gosummaries.kmeans} \alias{gosummaries.kmeans} \title{Prepare gosummaries object based on k-means results} diff --git a/man/gosummaries.matrix.Rd b/man/gosummaries.matrix.Rd index 95e3a03..b807888 100644 --- a/man/gosummaries.matrix.Rd +++ b/man/gosummaries.matrix.Rd @@ -1,4 +1,5 @@ -% Generated by roxygen2 (4.0.2): do not edit by hand +% Generated by roxygen2 (4.1.1): do not edit by hand +% Please edit documentation in R/GOsummaries.R \name{gosummaries.matrix} \alias{gosummaries.matrix} \title{Prepare gosummaries object based on Multi Dimensional Scaling (MDS) results} diff --git a/man/gosummaries.prcomp.Rd b/man/gosummaries.prcomp.Rd index 8af9786..d67c8bd 100644 --- a/man/gosummaries.prcomp.Rd +++ b/man/gosummaries.prcomp.Rd @@ -1,4 +1,5 @@ -% Generated by roxygen2 (4.0.2): do not edit by hand +% Generated by roxygen2 (4.1.1): do not edit by hand +% Please edit documentation in R/GOsummaries.R \name{gosummaries.prcomp} \alias{gosummaries.prcomp} \title{Prepare gosummaries object based on PCA results} diff --git a/man/metabolomic_example.Rd b/man/metabolomic_example.Rd index 7d5bb3c..415f627 100644 --- a/man/metabolomic_example.Rd +++ b/man/metabolomic_example.Rd @@ -1,4 +1,5 @@ -% Generated by roxygen2 (4.0.2): do not edit by hand +% Generated by roxygen2 (4.1.1): do not edit by hand +% Please edit documentation in R/exampleDatasets.R \docType{data} \name{metabolomic_example} \alias{metabolomic_example} diff --git a/man/metagenomic_example.Rd b/man/metagenomic_example.Rd index a36e8d9..9ac7521 100644 --- a/man/metagenomic_example.Rd +++ b/man/metagenomic_example.Rd @@ -1,4 +1,5 @@ -% Generated by roxygen2 (4.0.2): do not edit by hand +% Generated by roxygen2 (4.1.1): do not edit by hand +% Please edit documentation in R/exampleDatasets.R \docType{data} \name{metagenomic_example} \alias{metagenomic_example} diff --git a/man/panel_boxplot.Rd b/man/panel_boxplot.Rd index 57f708e..8d156bb 100644 --- a/man/panel_boxplot.Rd +++ b/man/panel_boxplot.Rd @@ -1,4 +1,5 @@ -% Generated by roxygen2 (4.0.2): do not edit by hand +% Generated by roxygen2 (4.1.1): do not edit by hand +% Please edit documentation in R/GOsummaries.R \name{panel_boxplot} \alias{panel_boxplot} \alias{panel_boxplot_classes} diff --git a/man/plot.gosummaries.Rd b/man/plot.gosummaries.Rd index 5abe603..e6c7c34 100644 --- a/man/plot.gosummaries.Rd +++ b/man/plot.gosummaries.Rd @@ -1,4 +1,5 @@ -% Generated by roxygen2 (4.0.2): do not edit by hand +% Generated by roxygen2 (4.1.1): do not edit by hand +% Please edit documentation in R/GOsummaries.R \name{plot.gosummaries} \alias{plot.gosummaries} \title{Plot the GOsummaries figure} diff --git a/man/plotWordcloud.Rd b/man/plotWordcloud.Rd index 7b8eff9..14b9008 100644 --- a/man/plotWordcloud.Rd +++ b/man/plotWordcloud.Rd @@ -1,4 +1,5 @@ -% Generated by roxygen2 (4.0.2): do not edit by hand +% Generated by roxygen2 (4.1.1): do not edit by hand +% Please edit documentation in R/wordcloud.R \name{plotWordcloud} \alias{plotWordcloud} \title{Plot a wordcloud given words and frequencies} diff --git a/man/tissue_example.Rd b/man/tissue_example.Rd index 05cac9a..7c58393 100644 --- a/man/tissue_example.Rd +++ b/man/tissue_example.Rd @@ -1,4 +1,5 @@ -% Generated by roxygen2 (4.0.2): do not edit by hand +% Generated by roxygen2 (4.1.1): do not edit by hand +% Please edit documentation in R/exampleDatasets.R \docType{data} \name{tissue_example} \alias{gs_kmeans}