boxplot.R:

added title arguments of x and group_by;
small changes in validation steps and description;
naming the lists;

boxplot.Rmd:
adapted the part for statical report;
added download option;
combined reactives to one single reactive outputting a data frame

visualization_function:
adapted function to accept a dataframe as input and axestitles

NAMESPACE

 # Generated by roxygen2: do not edit by hand
 
+export("%<>%")
+export("%>%")
 export(.bar_plot)
 export(.scatter_plot)
 export(.violin_plot)
 export(boxplot)
 export(plotly_boxplot)
+importFrom(magrittr,"%<>%")
+importFrom(magrittr,"%>%")

R/boxplot.R

-#' Renders a boxplot for cluster characterization
+#' Renders a boxplot
 #'
 #' @param object A \linkS4class{i2dash::i2dashboard} object.
 #' @param x Numeric observations for the boxplot. In case of a named list, a dropdown menu will be provided in the interactive mode.
@@ -6,21 +6,26 @@
 #' @param title The title of the components junk.
 #'
 #' @return A string containing markdown code for the rendered component.
-#'
 #' @export
-boxplot <- function(object, x, group_by, title = NULL) {
+boxplot <- function(object, x, group_by = NULL, title = NULL, title_x = NULL, title_group_by = NULL) {
   # Create random env id
   env_id <- paste0("env_", stringi::stri_rand_strings(1, 6, pattern = "[A-Za-z0-9]"))
 
+  # Create list if element is not a list already
   if(!is.list(x)) x <- list(x)
-  if(!is.list(group_by)) group_by <- list(group_by)
+  if(!is.list(group_by) & !is.null(group_by)) group_by <- list(group_by)
+
+  # name the lists
+  if(is.null(names(group_by)) & !is.null(group_by)) group_by %<>% magrittr::set_names("group")
+  if(is.null(names(x))) x %<>% magrittr::set_names("sample")
 
   # Validate input
   if(!all(sapply(x, is.numeric))) stop("'x' should only contain numerical values.")
-  if(!all(sapply(cluster, is.factor))) stop("'cluster' should only contain factorial values.")
+  if(!all(sapply(group_by, is.factor)) & !is.null(group_by)) stop("'group_by' should only contain factorial values.")
 
   # Create component environment
   env <- new.env()
+
   env$x_selection <- FALSE
   env$group_by_selection <- FALSE
 
@@ -30,6 +35,9 @@ boxplot <- function(object, x, group_by, title = NULL) {
   env$group_by <- group_by
   env$group_by_selection <- length(env$group_by) > 1
 
+  env$title_x <- title_x
+  env$title_group_by <- title_group_by
+
   # save environment object
   saveRDS(env, file = file.path(object@workdir, "envs", paste0(env_id, ".rds")))
 

inst/templates/boxplot.Rmd

@@ -9,6 +9,102 @@
 is_shiny <- identical(knitr::opts_knit$get("rmarkdown.runtime"), "shiny")
 ```
 
+### {{ title }}
+
+<!-- Component created on {{ date }} -->
+
+```{r}
+{{ env_id }} = readRDS("envs/{{ env_id }}.rds")
+
+is_shiny <- identical(knitr::opts_knit$get("rmarkdown.runtime"), "shiny")
+```
+
+```{r, eval=!is_shiny}
+# set variables
+x <- {{ env_id }}$x[1]
+group_by <- {{ env_id }}$group_by[1]
+if(is.null(group_by)){
+  df <- data.frame(x)
+} else {
+  df <- data.frame(x, group_by)
+}
+
+# Provide data download
+i2dash::embed_var(df)
+
+# Render plot
+i2dash.scrnaseq::plotly_boxplot(df = df, group_by = {{ env_id }}$group_by, title_x = {{ env_id }}$title_x, title_group_by = {{ env_id }}$title_group_by)
+```
+
+```{r, eval=is_shiny}
+ui_list <- list()
+
+# selection field for x
+if ({{ env_id }}$x_selection) {
+  ui_list <- rlist::list.append(ui_list,
+                                selectInput("select_x_{{ env_id }}", label = "Select observations:",
+                                            choices = names({{ env_id }}$x)))
+}
+
+# selection field for group_by
+if ({{ env_id }}$group_by_selection) {
+  ui_list <- rlist::list.append(ui_list,
+                                selectInput("select_group_by_{{ env_id }}", label = "Group observations by:",
+                                            choices = names({{ env_id }}$group_by)))
+}
+
+# download_link
+ui_list <- rlist::list.append(ui_list, tags$div(tags$br(), downloadButton('downloadData_{{ env_id }}', 'Download data')))
+
+#
+# Create reactive dataframe
+#
+df_{{ env_id }} <- shiny::reactive({
+  
+  if( !{{ env_id }}$x_selection ) {
+    x <- {{ env_id }}$x[1]
+  } else {
+    x <- {{ env_id }}$x[input$select_x_{{ env_id }}]
+  }
+
+  if( !{{ env_id }}$group_by_selection ) {
+    group_by <- {{ env_id }}$group_by[1]
+  } else {
+    group_by <- {{ env_id }}$group_by[input$select_group_by_{{ env_id }}]
+  }
+
+  if(is.null(group_by)){
+    df <- data.frame(x)
+  } else {
+    df <- data.frame(x, group_by)
+  }
+  return(df)
+  })
+
+#
+# Download
+#
+output$downloadData_{{ env_id }} <- downloadHandler(
+  filename =  paste('data-', Sys.Date(), '.csv', sep=''),
+  content = function(file) {
+    write.csv(df_{{ env_id }}(), file)
+  }
+)
+
+#
+# Output
+#
+output$plot_{{ env_id }} <- plotly::renderPlotly(
+  i2dash.scrnaseq::plotly_boxplot(df = df_{{ env_id }}(), group_by = {{ env_id }}$group_by, title_x = {{ env_id }}$title_x, title_group_by = {{ env_id }}$title_group_by)
+)
+
+shiny::fillCol(flex = c(NA, 1),
+        do.call(shiny::inputPanel, ui_list),
+        plotly::plotlyOutput("plot_{{ env_id }}", height = "100%")
+)
+```
+
+
 ```{r, eval=!is_shiny}
 # set variables
 x <- {{ env_id }}$x[[1]]

man/boxplot.Rd

@@ -2,9 +2,10 @@
 % Please edit documentation in R/boxplot.R
 \name{boxplot}
 \alias{boxplot}
-\title{Renders a boxplot for cluster characterization}
+\title{Renders a boxplot}
 \usage{
-boxplot(object, x, group_by, title = NULL)
+boxplot(object, x, group_by = NULL, title = NULL, title_x = NULL,
+  title_group_by = NULL)
 }
 \arguments{
 \item{object}{A \linkS4class{i2dash::i2dashboard} object.}
@@ -19,5 +20,5 @@ boxplot(object, x, group_by, title = NULL)
 A string containing markdown code for the rendered component.
 }
 \description{
-Renders a boxplot for cluster characterization
+Renders a boxplot
 }

man/dot-violin_plot.Rd

@@ -2,7 +2,7 @@
 % Please edit documentation in R/visualization_functions.R
 \name{.violin_plot}
 \alias{.violin_plot}
-\title{Render a box plot}
+\title{Render a violin plot}
 \usage{
 .violin_plot(x, y)
 }
@@ -15,5 +15,5 @@
 A list with 1. the plotly object & 2. the data frame used in the plot
 }
 \description{
-Render a box plot
+Render a violin plot
 }

man/grapes-greater-than-grapes.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/reexports.R
+\name{\%>\%}
+\alias{\%>\%}
+\title{magrittr forward-pipe operator}
+\description{
+See \code{\link[magrittr]{\%>\%}}.
+}

man/grapes-less-than-greater-than-grapes.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/reexports.R
+\name{\%<>\%}
+\alias{\%<>\%}
+\title{magrittr forward-backward-pipe operator}
+\description{
+See \code{\link[magrittr]{\%<>\%}}.
+}

man/multiplot.Rd

@@ -4,16 +4,16 @@
 \alias{multiplot}
 \title{Renders a Sequence saturation plot}
 \usage{
-multiplot(object, plot_title, x, y, color_by)
+multiplot(object, x, y, title = "Multiplot", colour_by = NULL)
 }
 \arguments{
-\item{plot_title}{The title of the Component}
-
 \item{x}{A list with the x-axis values. If it is a nested list, a dropdown-field will be provided in the interactive mode.}
 
 \item{y}{A list with the y-axis values. If it is a nested list, a dropdown-field will be provided in the interactive mode.}
 
-\item{color_by}{A list with the color_by values. If it is a nested list, a dropdown-field will be provided in the interactive mode.}
+\item{colour_by}{A list with the color_by values. If it is a nested list, a dropdown-field will be provided in the interactive mode.}
+
+\item{plot_title}{The title of the Component}
 }
 \value{
 A string containing markdown code for the rendered textbox

man/plotly_boxplot.Rd

@@ -4,16 +4,17 @@
 \alias{plotly_boxplot}
 \title{Render a box plot with plotly.}
 \usage{
-plotly_boxplot(x, group_by = NULL, title = "", group_by_title = NULL)
+plotly_boxplot(df, group_by = NULL, title_x = NULL,
+  title_group_by = NULL)
 }
 \arguments{
-\item{x}{Numeric observations for the boxplot.}
+\item{df}{A dataframe containing the data fo the boxplot.}
 
 \item{group_by}{A factor, by which observations can optionally be grouped.}
 
-\item{title}{A title that describes the observations.}
+\item{title_x}{A title that describes the observations.}
 
-\item{group_by_title}{A title that describes the grouping factor.}
+\item{title_group_by}{A title that describes the grouping factor.}
 }
 \value{
 An object of class \code{plotly}.

man/sequence_saturation.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/sequence_saturation.R
+% Please edit documentation in R/dimension_reduction.R, R/sequence_saturation.R
 \name{sequence_saturation}
 \alias{sequence_saturation}
 \title{Renders a Sequence saturation plot}
 \usage{
+sequence_saturation(object, x, y, colour_by = NULL, labels = NULL,
+  title = "Sequencing saturation")
+
 sequence_saturation(object, x, y, colour_by = NULL, labels = NULL,
   title = "Sequencing saturation")
 }
@@ -18,11 +21,23 @@ sequence_saturation(object, x, y, colour_by = NULL, labels = NULL,
 
 \item{labels}{A list with sample names, that should be of the same length as x and y.}
 
+\item{title}{A title that will be displayed on top.}
+
+\item{red_dim}{List with reduced dimensions as data.frames.}
+
+\item{coulor_by}{A factor that will be mapped to colours.In case of a nested list, a dropdown menu will be provided in the interactive mode.}
+
+\item{object}{A \linkS4class{i2dash::i2dashboard} object.}
+
 \item{title}{A title that will be displayed on top.}
 }
 \value{
+A string containing markdown code for the rendered textbox
+
 A string containing markdown code for the rendered textbox
 }
 \description{
+Renders a Sequence saturation plot
+
 Renders a Sequence saturation plot
 }