cleanup formatting a bit

Author: pimentel

NAMESPACE

@@ -12,14 +12,17 @@ export(basic_filter)
 export(bs_sigma_summary)
 export(counts_to_fpkm)
 export(counts_to_tpm)
+export(enclosed_brush)
 export(get_quantile)
 export(melt_bootstrap_sleuth)
 export(models)
 export(norm_factors)
 export(plot_bootstrap)
+export(plot_group_density)
 export(plot_ma)
 export(plot_mean_var)
 export(plot_pca)
+export(plot_sample_density)
 export(plot_scatter)
 export(plot_transcript)
 export(plot_transcript_variability)

R/plots.R

@@ -127,9 +127,11 @@ plot_pca <- function(obj,
 #' @param trans a string pointing to a function to use for the transformation.
 #' @param grouping a string from the columns of \code{sample_to_covariates} in
 #' the sleuth object for which to group and color by
-#' @param offset the offset so that transformations such as log don't compute -Inf. If NULL, then will not add an offset (one could also use 
-#' @param
-plot_gorup_density <- function(obj,
+#' @param offset the offset so that transformations such as log don't compute
+#' -Inf. If NULL, then will not add an offset
+#' @return a \code{ggplot2} object
+#' @export
+plot_group_density <- function(obj,
   use_filtered = TRUE,
   units = 'est_counts',
   trans = 'log',
@@ -166,6 +168,21 @@ plot_gorup_density <- function(obj,
   p
 }
 
+#' Plot sample density
+#'
+#' Plot the density of one particular sample
+#'
+#' @param obj a \code{sleuth} object
+
+#' @param which_sample a character string matching a sample in
+#' \code{obj$sample_to_covariates}
+#' @param use_filtered if TRUE, use filtered data. Otherwise use all data
+#' @param units either \code{'est_counts'} or \code{'tpm'}
+#' @param trans a string pointing to a function to use for the transformation.
+#' @param offset the offset so that transformations such as log don't compute
+#' -Inf. If NULL, then will not add an offset
+#' @return a \code{ggplot2} object
+#' @export
 plot_sample_density <- function(obj,
   which_sample = obj$sample_to_covariates$sample[1],
   use_filtered = TRUE,
@@ -245,7 +262,7 @@ plot_scatter <- function(obj,
     sample_y <- paste0( trans, '( ', sample_y)
   }
 
-  if ( offset != 0 ) {
+  if ( (!is.null(offset) && !is.na(offset)) && offset != 0 ) {
     off <- deparse(eval(offset))
     sample_x <- paste0(sample_x, ' + ', off)
     sample_y <- paste0(sample_y, ' + ', off)

R/shiny.R

@@ -29,7 +29,39 @@ sleuth_interact <- function(obj, select_trans = FALSE, ...) {
     a('sleuth', href = 'http://pimentel.github.io/sleuth', target = '_blank',
       style = 'color: black;'),
 
-    tabPanel('diagnostics'),
+    tabPanel('diagnostics',
+      ####
+        fluidRow(
+          column(4,
+            selectInput('sample_x', label = 'x-axis: ',
+              choices = samp_names,
+              selected = samp_names[1])
+            ),
+          column(4,
+            selectInput('sample_y', label = 'y-axis: ',
+              choices = samp_names,
+              selected = samp_names[2])
+            ),
+          column(2,
+            textInput('trans', label = 'transform: ',
+              value = 'log')),
+          column(2,
+            numericInput('scatter_offset', label = 'offset: ', value = 1))
+          ),
+        fluidRow(
+          column(2,
+            selectInput('scatter_units', label = 'units: ',
+              choices = c('est_counts', 'tpm'),
+              selected = 'est_counts')),
+          column(2,
+            checkboxInput('scatter_filt', label = 'filter',
+              value = TRUE)),
+          column(2,
+            numericInput('scatter_alpha', label = 'opacity:', value = 0.2,
+              min = 0, max = 1, step = 0.01))
+          ),
+        plotOutput('scatter')
+      ),
 
     navbarMenu('summaries',
       ####
@@ -137,38 +169,6 @@ sleuth_interact <- function(obj, select_trans = FALSE, ...) {
         plotOutput('mv_plt')
         ),
 
-      ####
-      tabPanel('scatter plots',
-        fluidRow(
-          column(4,
-            selectInput('sample_x', label = 'x-axis: ',
-              choices = samp_names,
-              selected = samp_names[1])
-            ),
-          column(4,
-            selectInput('sample_y', label = 'y-axis: ',
-              choices = samp_names,
-              selected = samp_names[2])
-            ),
-          column(2,
-            textInput('trans', label = 'transform: ',
-              value = 'log')),
-          column(2,
-            numericInput('scatter_alpha', label = 'opacity:', value = 0.2,
-              min = 0, max = 1, step = 0.01))
-          ),
-        fluidRow(
-          column(2,
-            selectInput('scatter_units', label = 'units: ',
-              choices = c('est_counts', 'tpm'),
-              selected = 'est_counts')),
-          column(2,
-            checkboxInput('scatter_filt', label = 'filter',
-              value = TRUE)),
-          column(2,
-            numericInput('scatter_offset', label = 'offset: ', value = 1))
-          ),
-        plotOutput('scatter')),
 
       ####
       tabPanel('DE table',
@@ -200,7 +200,7 @@ sleuth_interact <- function(obj, select_trans = FALSE, ...) {
     output$summary_dt <- renderDataTable(summary(obj))
 
     output$condition_density <- renderPlot({
-      plot_density(obj,
+      plot_group_density(obj,
         grouping = input$cond_dens_grp,
         units = input$cond_dens_units,
         use_filtered = input$cond_dens_filt,
@@ -223,7 +223,8 @@ sleuth_interact <- function(obj, select_trans = FALSE, ...) {
       plot_scatter(obj, input$sample_x, input$sample_y,
         trans = input$trans, point_alpha = input$scatter_alpha,
         units = input$scatter_units,
-        use_filtered = input$scatter_filt)
+        use_filtered = input$scatter_filt,
+        offset = input$scatter_offset)
     })
 
     ###
@@ -353,6 +354,7 @@ sleuth_interact <- function(obj, select_trans = FALSE, ...) {
   shinyApp(ui = p_layout, server = server_fun)
 }
 
+#' @export
 enclosed_brush <- function(df, brush) {
   xvar <- brush$mapping$x
   yvar <- brush$mapping$y

man/plot_group_density.Rd

@@ -0,0 +1,32 @@
+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/plots.R
+\name{plot_group_density}
+\alias{plot_group_density}
+\title{Plot density}
+\usage{
+plot_group_density(obj, use_filtered = TRUE, units = "est_counts",
+  trans = "log", grouping = setdiff(colnames(obj$sample_to_covariates),
+  "sample"), offset = 1)
+}
+\arguments{
+\item{obj}{a \code{sleuth} object}
+
+\item{use_filtered}{if TRUE, use filtered data. otherwise use all data}
+
+\item{units}{either 'est_counts' or 'tpm'}
+
+\item{trans}{a string pointing to a function to use for the transformation.}
+
+\item{grouping}{a string from the columns of \code{sample_to_covariates} in
+the sleuth object for which to group and color by}
+
+\item{offset}{the offset so that transformations such as log don't compute
+-Inf. If NULL, then will not add an offset}
+}
+\value{
+a \code{ggplot2} object
+}
+\description{
+Plot the density of a some grouping
+}
+

man/plot_sample_density.Rd

@@ -0,0 +1,31 @@
+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/plots.R
+\name{plot_sample_density}
+\alias{plot_sample_density}
+\title{Plot sample density}
+\usage{
+plot_sample_density(obj, which_sample = obj$sample_to_covariates$sample[1],
+  use_filtered = TRUE, units = "est_counts", trans = "log", offset = 1)
+}
+\arguments{
+\item{obj}{a \code{sleuth} object}
+
+\item{which_sample}{a character string matching a sample in
+\code{obj$sample_to_covariates}}
+
+\item{use_filtered}{if TRUE, use filtered data. Otherwise use all data}
+
+\item{units}{either \code{'est_counts'} or \code{'tpm'}}
+
+\item{trans}{a string pointing to a function to use for the transformation.}
+
+\item{offset}{the offset so that transformations such as log don't compute
+-Inf. If NULL, then will not add an offset}
+}
+\value{
+a \code{ggplot2} object
+}
+\description{
+Plot the density of one particular sample
+}
+