new commit to merge files after talk

Merge branch 'master' of https://gitlab.gwdg.de/loosolab/software/i2dash.scrnaseq

# Conflicts:
#	NAMESPACE
#	man/dot-box_plot.Rd

DESCRIPTION

@@ -12,3 +12,8 @@ License: What license is it under?
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 6.1.1
+Imports: 
+    stringi,
+    plotly,
+    shiny,
+    knitr

NAMESPACE

 # Generated by roxygen2: do not edit by hand
 
 export(.bar_plot)
-export(.box_plot)
 export(.scatter_plot)
 export(.violin_plot)
+export(boxplot)
+export(plotly_boxplot)

R/boxplot.R

+#' Renders a boxplot for cluster characterization
+#'
+#' @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.
+#' @param group_by A factor, by which observations can optionally be grouped. In case of a named list, a dropdown menu will be provided in the interactive mode.
+#' @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) {
+  # Create random env id
+  env_id <- paste0("env_", stringi::stri_rand_strings(1, 6, pattern = "[A-Za-z0-9]"))
+
+  if(!is.list(x)) x <- list(x)
+  if(!is.list(group_by)) group_by <- list(group_by)
+
+  # 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.")
+
+  # Create component environment
+  env <- new.env()
+  env$x_selection <- FALSE
+  env$group_by_selection <- FALSE
+
+  env$x <- x
+  env$x_selection <- length(env$x) > 1
+
+  env$group_by <- group_by
+  env$group_by_selection <- length(env$group_by) > 1
+
+  # save environment object
+  saveRDS(env, file = file.path(object@workdir, "envs", paste0(env_id, ".rds")))
+
+  # Expand component
+  timestamp <- Sys.time()
+  expanded_component <- knitr::knit_expand(file = system.file("templates", "boxplot.Rmd", package = "i2dash.scrnaseq"), title = title, env_id = env_id, date = timestamp)
+  return(expanded_component)
+}

R/cluster_characterization_boxplot.R

-#' Renders a boxplot for cluster characterization
-#'
-#' @param object A \linkS4class{i2dash::i2dashboard} object.
-#' @param cluster Values for the membership to clusters. In case of a nested list, a dropdown menu will be provided in the interactive mode.
-#' @param x Numeric values mapped to the x-axis. In case of a nested list, a dropdown menu will be provided in the interactive mode. If x is NULL then a barplot for "Number of cells" per cluster will be created. If x is not NULL a barplot for "Fraction per cell" per cluster will be created.
-#' @param title A title that will be displayed on top.
-#'
-#' @return A string containing markdown code for the rendered textbox
-cluster_characterization_boxplot <- function(object, x, cluster, title = "Characterization of clusters") {
-  # Create random env id
-  env_id <- paste0("env_", stringi::stri_rand_strings(1, 6, pattern = "[A-Za-z0-9]"))
-
-  # validate input, create environment variables, save environment object
-  .validate_input_cluster_characterizatio_boxplot(object@workdir, env_id, x, cluster)
-
-  timestamp <- Sys.time()
-  expanded_component <- knitr::knit_expand(file = system.file("templates", "cluster_characterization_boxplot_template.Rmd", package = "i2dash.scrnaseq"), title = title, env_id = env_id, date = timestamp)
-  return(expanded_component)
-}
-
-.validate_input_cluster_characterizatio_boxplot <- function(workdir, env_id, x, cluster) {
-  env <- new.env()
-  env$x_selection <- FALSE
-  env$cluster_selection <- FALSE
-
-  # Check existence of cluster
-  if(is.null(cluster)) stop("cluster is required.")
-  if(is.null(x)) stop("x is required.")
-
-  # Create lists if needed
-  if(!is.list(x)) x <- list(x)
-  if(!is.list(cluster)) cluster <- list(cluster)
-
-  # should I use magrittr::%<>% ?
-  # name the lists
-  library(magrittr)
-  if(is.null(names(cluster))) x %<>% magrittr::set_names("clustering.1")
-  if(is.null(names(x))) x %<>% magrittr::set_names("x")
-
-  # Check validity
-  if(!all(sapply(cluster, is.factor))) stop("'cluster' should only contain factorial values.")
-  if(!all(sapply(x, is.numeric))) stop("'x' should only contain numerical values.")
-
-  # Check if lengths in a list are the same and if x and y and label and color_by are the same length
-  #if(length(unique(sapply(x, length))) != 1) stop("list x should contain elements with the same length.")
-  #if(length(unique(sapply(y, length))) != 1) stop("list y should contain elements with the same length.")
-
-  #if(!identical(length(x[[1]]), length(y[[1]]))) stop("all arguments should be of the the same length.")
-  #if(!identical(length(x[[1]]), length(colour_by[[1]])) & !is.null(colour_by)) stop("all arguments should be of the the same length.")
-  #if(!identical(length(x[[1]]), length(labels[[1]])) & !is.null(labels)) stop("all arguments should be of the the same length.")
-
-  # Add objects to env
-  env$x <- x
-  env$x_selection <- length(env$x) > 1
-
-  env$cluster <- cluster
-  env$cluster_selection <- length(env$cluster) > 1
-
-  # save environment as rds-object
-  saveRDS(env, file = file.path(workdir, "envs", paste0(env_id, ".rds")))
-  print("validation TRUE")
-}

R/sequence_saturation.R

@@ -26,10 +26,6 @@ sequence_saturation <- function(object, x, y, colour_by = NULL, labels = NULL, t
   env$y_selection <- FALSE
   env$colour_by_selection <- FALSE
 
-  # Check existence of x and y
-  if(is.null(x)) stop("x is required.")
-  if(is.null(y)) stop("y is required.")
-
   # Create lists if needed
   if(!is.list(x)) x <- list(x)
   if(!is.list(y)) y <- list(y)

R/visualization_functions.R

@@ -126,25 +126,20 @@
 
 }
 
-#' Render a box plot
+#' Render a box plot with plotly.
 #'
-#' @param cluster Values for the membership to clusters. In case of a nested list, a dropdown menu will be provided in the interactive mode.
-#' @param x Numeric values mapped to the x-axis. In case of a nested list, a dropdown menu will be provided in the interactive mode.
+#' @param x Numeric observations for the boxplot.
+#' @param group_by A factor, by which observations can optionally be grouped.
+#' @param title A title that describes the observations.
+#' @param group_by_title A title that describes the grouping factor.
 #'
-#' @return A list with 1. the plotly object & 2. the data frame used in the plot
+#' @return An object of class \code{plotly}.
 #' @export
-.box_plot <- function(cluster, x){
-  df <- data.frame(cluster, x)
-
-  # plotly
-  title <- "Detected genes"
-  p <- plotly::plot_ly(df, y = df[[1]], x = df[[2]], type = "box", name = df[[1]])
-  p <- plotly::layout(p,
-                      xaxis = list(title=title, showline = T),
-                      yaxis = list(title="Cluster", showline = T, showticklabels = T),
-                      showlegend = T
-  )
-  return(list("plot" = p, "df" = df))
+plotly_boxplot <- function(x, group_by = NULL, title = "", group_by_title = NULL){
+  plotly::plot_ly(x = x, y = group_by, type = "box", name = title) %>%
+    plotly::layout(xaxis = list(title = title, showline = T),
+                   yaxis = list(title = group_by_title, showline = T, showticklabels = T),
+                   showlegend = T)
 }
 
 #' Render a violin plot

inst/templates/boxplot.Rmd

+
+### {{ 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 }}$group_by[[1]]
+
+# Provide data download
+# data.frame(x, group_by) %>%
+#   i2dash::embed_var()
+
+# Render plot
+i2dash.scrnaseq::plotly_box_plot(x = x, group_by = group_by)
+```
+
+```{r, eval=is_shiny}
+ui_list <- list()
+
+# selection field for x
+if ({{ env_id }}$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 }}$group_by)))
+}
+
+#
+# Handle inputs
+#
+if( !{{ env_id }}$x_selection ) {
+  x_{{ env_id }} <- shiny::reactive({
+    {{ env_id }}$x[[1]]
+  })
+} else {
+  x_{{ env_id }} <- shiny::reactive({
+    {{ env_id }}$x[[input$select_x_{{ env_id }}]]
+  })
+}
+
+if( !{{ env_id }}$group_by_selection ) {
+  group_by_{{ env_id }} <- shiny::reactive({
+    {{ env_id }}$group_by[[1]]
+  })
+} else {
+  group_by_{{ env_id }} <- shiny::reactive({
+    {{ env_id }}$group_by[[input$select_group_by_{{ env_id }}]]
+  })
+}
+
+#
+# Output
+#
+output$plot_{{ env_id }} <- plotly::renderPlotly(
+  i2dash.scrnaseq::plotly_box_plot(x = x_{{ env_id }}(), group_by = group_by_{{ env_id }}())
+)
+
+shiny::fillCol(flex = c(NA, 1),
+        do.call(shiny::inputPanel, ui_list),
+        plotly::plotlyOutput("plot_{{ env_id }}", height = "100%")
+)
+```

inst/templates/cluster_characterization_boxplot_template.Rmd

-
-### {{ title }}
-
-<!-- Component created on {{ date }} -->
-
-```{r}
-{{ env_id }} = readRDS("envs/{{ env_id }}.rds")
-
-is_shiny <- identical(knitr::opts_knit$get("rmarkdown.runtime"), "shiny")
-```
-
-```{r, eval=!is_shiny}
-
-```
-
-```{r, eval=is_shiny}
-df <- data.frame({{ env_id }}$cluster[1], {{ env_id }}$x)
-#print(df)
-title <- "Detected genes"
-p <- plotly::plot_ly(df, y = df[[1]], x = df[[2]], type = "box", name = df[[1]])
-p <- plotly::layout(p,
-                    xaxis = list(title=title, showline = T),
-                    yaxis = list(title="Cluster", showline = T, showticklabels = T),
-                    showlegend = T
-)
-p
-```
-
-***
-
-Plot description:
-
-Sequencing is called *saturated* when generating more sequencing output from a cDNA library does not substantially increase the number of detected features in a sample. Since the number of detected features can act as a technical confounder, and thereby drive substructure in the data, it is advisable to aim for a saturated sequencing by either adding more sequencing output or decreasing the number of samples until saturation is achieved. [@zhang_one_2018] gives advise on how to choose the optimal cell number given a fixed sequencing budget
-
-

man/cluster_characterization_boxplot.Rd → man/boxplot.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/cluster_characterization_boxplot.R
-\name{cluster_characterization_boxplot}
-\alias{cluster_characterization_boxplot}
+% Please edit documentation in R/boxplot.R
+\name{boxplot}
+\alias{boxplot}
 \title{Renders a boxplot for cluster characterization}
 \usage{
-cluster_characterization_boxplot(object, x, cluster,
-  title = "Characterization of clusters")
+boxplot(object, x, group_by, title = NULL)
 }
 \arguments{
 \item{object}{A \linkS4class{i2dash::i2dashboard} object.}
 
-\item{x}{Numeric values mapped to the x-axis. In case of a nested list, a dropdown menu will be provided in the interactive mode. If x is NULL then a barplot for "Number of cells" per cluster will be created. If x is not NULL a barplot for "Fraction per cell" per cluster will be created.}
+\item{x}{Numeric observations for the boxplot. In case of a named list, a dropdown menu will be provided in the interactive mode.}
 
-\item{cluster}{Values for the membership to clusters. In case of a nested list, a dropdown menu will be provided in the interactive mode.}
+\item{group_by}{A factor, by which observations can optionally be grouped. In case of a named list, a dropdown menu will be provided in the interactive mode.}
 
-\item{title}{A title that will be displayed on top.}
+\item{title}{The title of the components junk.}
 }
 \value{
-A string containing markdown code for the rendered textbox
+A string containing markdown code for the rendered component.
 }
 \description{
 Renders a boxplot for cluster characterization

man/dot-box_plot.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/visualization_functions.R
-\name{.box_plot}
-\alias{.box_plot}
-\title{Render a box plot}
-\usage{
-.box_plot(cluster, x)
-}
-\arguments{
-\item{cluster}{Values for the membership to clusters. In case of a nested list, a dropdown menu will be provided in the interactive mode.}
-
-\item{x}{Numeric values mapped to the x-axis. In case of a nested list, a dropdown menu will be provided in the interactive mode.}
-}
-\value{
-A list with 1. the plotly object & 2. the data frame used in the plot
-}
-\description{
-Render a box plot
-}

man/multiplot.Rd

@@ -4,16 +4,16 @@
 \alias{multiplot}
 \title{Renders a Sequence saturation plot}
 \usage{
-multiplot(object, x, y, title = "Multiplot", colour_by = NULL)
+multiplot(object, plot_title, x, y, color_by)
 }
 \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{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}
+\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.}
 }
 \value{
 A string containing markdown code for the rendered textbox

man/plotly_boxplot.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/visualization_functions.R
+\name{plotly_boxplot}
+\alias{plotly_boxplot}
+\title{Render a box plot with plotly.}
+\usage{
+plotly_boxplot(x, group_by = NULL, title = "", group_by_title = NULL)
+}
+\arguments{
+\item{x}{Numeric observations for the boxplot.}
+
+\item{group_by}{A factor, by which observations can optionally be grouped.}
+
+\item{title}{A title that describes the observations.}
+
+\item{group_by_title}{A title that describes the grouping factor.}
+}
+\value{
+An object of class \code{plotly}.
+}
+\description{
+Render a box plot with plotly.
+}

man/sequence_saturation.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/dimension_reduction.R, R/sequence_saturation.R
+% Please edit documentation in 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")
 }
@@ -21,23 +18,11 @@ 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
 }