From 28cc11e92173ef749580ef84ebb53f676c47b5d6 Mon Sep 17 00:00:00 2001 From: Schultheis Date: Tue, 23 Jul 2019 15:47:12 +0200 Subject: [PATCH] add namespace and documentation of {plot}_to_i2dash functions --- NAMESPACE | 3 +++ man/geneview_to_i2dash.Rd | 28 ++++++++++++++++++++++++++++ man/heatmap_to_i2dash.Rd | 28 ++++++++++++++++++++++++++++ man/scatterplot_to_i2dash.Rd | 32 ++++++++++++++++++++++++++++++++ 4 files changed, 91 insertions(+) create mode 100644 man/geneview_to_i2dash.Rd create mode 100644 man/heatmap_to_i2dash.Rd create mode 100644 man/scatterplot_to_i2dash.Rd diff --git a/NAMESPACE b/NAMESPACE index 8db88f5..bd434cf 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -15,10 +15,12 @@ export(featureSelector) export(featureSelectorUI) export(geneView) export(geneViewUI) +export(geneview_to_i2dash) export(global_cor_heatmap) export(global_cor_heatmapUI) export(heatmap) export(heatmapUI) +export(heatmap_to_i2dash) export(label) export(labelUI) export(limit) @@ -35,6 +37,7 @@ export(pca) export(pcaUI) export(scatterPlot) export(scatterPlotUI) +export(scatterplot_to_i2dash) export(set_logger) export(tobias_parser) export(transformation) diff --git a/man/geneview_to_i2dash.Rd b/man/geneview_to_i2dash.Rd new file mode 100644 index 0000000..a93c67e --- /dev/null +++ b/man/geneview_to_i2dash.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/i2dash.R +\name{geneview_to_i2dash} +\alias{geneview_to_i2dash} +\title{Prepare a geneview to be rendered with the i2dash package.} +\usage{ +geneview_to_i2dash(object, countTable, group_by, compId = NULL, + title = NULL, ...) +} +\arguments{ +\item{object}{A \linkS4class{i2dash::i2dashboard} object.} + +\item{countTable}{A matrix with features as rows and observations as columns. The rownames and columnnames should be provided and are used in buiding the heatmap.} + +\item{group_by}{A vector with values or a named list will be mapped to the y-axis. In case of a named list, a dropdown menu will be provided in the interactive mode. Note: The length of vectors x and y should be the same as well as the length of all vectors in case of a named list.} + +\item{compId}{(Optional) The component ID provided through add_component and used for linking components together.} + +\item{title}{(Optional) The title of the components chunk.} + +\item{(...)}{Further parameters which are compatible with wilsons create_scatterplot() method. See \code{\link[wilson::create_scatterplot()]{wilson}}.} +} +\value{ +A string containing markdown code for the rendered textbox +} +\description{ +Prepare a geneview to be rendered with the i2dash package. +} diff --git a/man/heatmap_to_i2dash.Rd b/man/heatmap_to_i2dash.Rd new file mode 100644 index 0000000..62cfb4f --- /dev/null +++ b/man/heatmap_to_i2dash.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/i2dash.R +\name{heatmap_to_i2dash} +\alias{heatmap_to_i2dash} +\title{Prepare a heatmap to be rendered with the i2dash package.} +\usage{ +heatmap_to_i2dash(object, countTable, group_by, compId = NULL, + title = NULL, ...) +} +\arguments{ +\item{object}{A \linkS4class{i2dash::i2dashboard} object.} + +\item{countTable}{A matrix with features as rows and observations as columns. The rownames and columnnames should be provided and are used in building the heatmap.} + +\item{group_by}{A vector with numerical values or a named list will be mapped to the y-axis. In case of a named list, a dropdown menu will be provided in the interactive mode. Note: The length of vectors x and y should be the same as well as the length of all vectors in case of a named list.} + +\item{compId}{(Optional) The component ID provided through add_component and used for linking components together.} + +\item{title}{(Optional) The title of the components chunk.} + +\item{(...)}{Further parameters which are compatible with wilsons create_scatterplot() method. See \code{\link[wilson::create_scatterplot()]{wilson}}.} +} +\value{ +A string containing markdown code for the rendered textbox +} +\description{ +Prepare a heatmap to be rendered with the i2dash package. +} diff --git a/man/scatterplot_to_i2dash.Rd b/man/scatterplot_to_i2dash.Rd new file mode 100644 index 0000000..83f5d86 --- /dev/null +++ b/man/scatterplot_to_i2dash.Rd @@ -0,0 +1,32 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/i2dash.R +\name{scatterplot_to_i2dash} +\alias{scatterplot_to_i2dash} +\title{Prepare a scatterplot to be rendered with the i2dash package.} +\usage{ +scatterplot_to_i2dash(object, x, y, colour_by = NULL, + expression = NULL, compId = NULL, title = NULL, ...) +} +\arguments{ +\item{object}{A \linkS4class{i2dash::i2dashboard} object.} + +\item{x}{A vector with numerical values or a named list will be mapped to the x-axis. In case of a named list, a dropdown menu will be provided in the interactive mode. Note: The length of vectors x and y should be the same as well as the length of all vectors in case of a named list.} + +\item{y}{A vector with numerical values or a named list will be mapped to the y-axis. In case of a named list, a dropdown menu will be provided in the interactive mode. Note: The length of vectors x and y should be the same as well as the length of all vectors in case of a named list.} + +\item{colour_by}{(Optional) A vector with factorial (= categorical coloring), numerical (= sequential colouring; can be forced to use categorical colouring by providing the parameter '"categorized" = TRUE') or character (= categorical colouring) values or a named list that will be used for colouring. In case of a named list, a dropdown menu will be provided in the interactive mode. Note: The length of the vector should be of the same length as x and y as well as the length of all vectors in case of a named list.} + +\item{expression}{(Optional) A matrix or dataframe with the same length of columns as 'x'. The sequence and number of the columns should be equal to the sequence and length of 'x'. The rownames represent the feature i.e. gene names and the values represent the expression level. Note: This feature is not compatible with the statical mode (parameter '"interactive" = TRUE'). Alternatively you can provide a vector as colour_by.} + +\item{compId}{(Optional) The component ID provided through add_component and used for linking components together.} + +\item{title}{(Optional) The title of the components chunk.} + +\item{(...)}{Further parameters which are compatible with wilsons create_scatterplot() method. See \code{\link[wilson::create_scatterplot()]{wilson}}.} +} +\value{ +A string containing markdown code for the rendered textbox +} +\description{ +Prepare a scatterplot to be rendered with the i2dash package. +}