Add fixed expression range support to 3D model coloring

rajewsky-lab · May 17, 2018 · b268c9b · b268c9b
1 parent 9b4b505
commit b268c9b
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Showing 4 changed files with 43 additions and 17 deletions.
diff --git a/functions.R b/functions.R
@@ -21,7 +21,7 @@
 # file:         functions.R
 # author(s):    Marcel Schilling <marcel.schilling@mdc-berlin.de>
 # created:      2017-02-23
-# last update:  2018-04-16
+# last update:  2018-04-23
 # license:      GNU Affero General Public License Version 3 (GNU AGPL v3)
 # purpose:      define functions for tomo-seq shiny app
 
@@ -30,6 +30,7 @@
 # change log (reverse chronological) #
 ######################################
 
+# 2018-04-23: added fixed expression range support to 3D model coloring
 # 2018-04-16: renamed y-axis limits inputs to expression range inputs
 # 2018-04-13: added sample shifts & stretches to 3D model coloring
 #             removed left-over code from user specified sample shift/strech support
@@ -2206,24 +2207,28 @@ generate.heatmap<-
     # end heatmap generation function definition
     }
 
-plot.model3d <- function(outline, cpm.fit = NULL){
+plot.model3d <- function(outline, cpm.fit = NULL, plot.options = character(0),
+                         manual.exprlim = NULL){
+
   if(is.null(cpm.fit)) outline %<>% mutate(cpm = NA)
   else
     outline %<>%
       left_join(distinct(., dp) %>%
                 mutate(cpm = predict(cpm.fit, dp)))
+  if(!("set.exprlim" %in% plot.options)) manual.exprlim <- NULL
+
   outline %>%
-  plot_ly(x = ~dp, y = ~lr, z = ~dv) %>%
-  add_lines(color = ~cpm, colors = params$colorscale.model3d) %>%
-  colorbar(title = params$colorlab.model3d) %>%
-  layout(title = params$plot.title.model3d,
-         scene = list(xaxis = list(title = params$dplab.model3d),
-                      yaxis = list(title = params$lrlab.model3d),
-                      zaxis = list(title = params$dvlab.model3d),
-                      aspectmode = "data",
-                      camera = list(eye = list(x = params$eye.model3d.dp,
-                                               y = params$eye.model3d.lr,
-                                               z = params$eye.model3d.dv))))}
+    plot_ly(x = ~dp, y = ~lr, z = ~dv) %>%
+    add_lines(color = ~cpm, colors = params$colorscale.model3d) %>%
+    colorbar(title = params$colorlab.model3d, limits = manual.exprlim) %>%
+    layout(title = params$plot.title.model3d,
+           scene = list(xaxis = list(title = params$dplab.model3d),
+                        yaxis = list(title = params$lrlab.model3d),
+                        zaxis = list(title = params$dvlab.model3d),
+                        aspectmode = "data",
+                        camera = list(eye = list(x = params$eye.model3d.dp,
+                                                 y = params$eye.model3d.lr,
+                                                 z = params$eye.model3d.dv))))}
 
 
     ##########################

diff --git a/params.R b/params.R
@@ -21,7 +21,7 @@
 # file:         params.R
 # author(s):    Marcel Schilling <marcel.schilling@mdc-berlin.de>
 # created:      2017-02-21
-# last update:  2018-04-16
+# last update:  2018-04-23
 # license:      GNU Affero General Public License Version 3 (GNU AGPL v3)
 # purpose:      define parameters for tomo-seq shiny app
 
@@ -30,6 +30,7 @@
 # change log (reverse chronological) #
 ######################################
 
+# 2018-04-23: added 3D model fixed expression range plot option
 # 2018-04-16: renamed y-axis limits inputs to expression range inputs
 # 2018-04-13: added 3D model gene name input default parameter
 #             added 3D model gene name input panel label parameter
@@ -487,6 +488,9 @@ if(!exists("params"))
       model3d.tab.title = "3D model",
       gene3d.input.label = "Gene/miRNA name",
       gene3d.input.default = "rpl-17",
+      plot.options3d =
+        c(`manually set expression range limis` = "set.exprlim"),
+      plot.options3d.input.default = c(),
 
 
   ##############

diff --git a/server.R b/server.R
@@ -21,7 +21,7 @@
 # file:         server.R
 # author(s):    Marcel Schilling <marcel.schilling@mdc-berlin.de>
 # created:      2017-02-21
-# last update:  2018-04-16
+# last update:  2018-04-23
 # license:      GNU Affero General Public License Version 3 (GNU AGPL v3)
 # purpose:      define back end for tomo-seq shiny app
 
@@ -30,6 +30,7 @@
 # change log (reverse chronological) #
 ######################################
 
+# 2018-04-23: added 3D expression range inputs
 # 2018-04-16: renamed y-axis limits inputs to expression range inputs
 # 2018-04-13: added 3D model gene name default
 #             replaced user specified sample shifts by defaults
@@ -155,6 +156,13 @@ function(input, output, session){
     renderUI(
       generate.gene.type.input(params$sample.description.input.default,
                                input$genotype))
+  output$manual.exprmin3d.input <-
+    renderUI(generate.manual.exprmin.input(input$plot.options3d,
+                                           id = "manual.exprmin3d"))
+  output$manual.exprmax3d.input <-
+    renderUI(generate.manual.exprmax.input(input$plot.options3d,
+                                           exprmin = input$manual.exprmin3d,
+                                           id = "manual.exprmax3d"))
 
   # assign gene list filtered gene profiles
   gene.profiles.filtered.gene.list<-
@@ -293,7 +301,9 @@ function(input, output, session){
                   filter(gene.name == input$gene3d,
                          genotype == input$genotype3d) %>%
                   fit.cpm(model.length = max(input.data$gonad.model$outline$dp),
-                          smoothing.span = input$span3d)))
+                          smoothing.span = input$span3d),
+        plot.options = input$plot.options3d,
+        manual.exprlim = c(input$manual.exprmin3d, input$manual.exprmax3d)))
 
   # assign gene annotation
   gene.annotation<-

diff --git a/ui.R b/ui.R
@@ -21,7 +21,7 @@
 # file:         ui.R
 # author(s):    Marcel Schilling <marcel.schilling@mdc-berlin.de>
 # created:      2017-02-21
-# last update:  2018-04-16
+# last update:  2018-04-23
 # license:      GNU Affero General Public License Version 3 (GNU AGPL v3)
 # purpose:      define front end for tomo-seq shiny app
 
@@ -30,6 +30,7 @@
 # change log (reverse chronological) #
 ######################################
 
+# 2018-04-23: added 3D model plot options input panel & expression range inputs
 # 2018-04-16: renamed y-axis limits inputs to expression range inputs
 # 2018-04-13: relabeled 3D model gene input panel
 #             removed sample shift input panel
@@ -483,6 +484,12 @@ fluidPage(
                      selectizeInput(inputId = "gene3d",
                                     label = h3(params$gene3d.input.label),
                                     choices  = NULL),
+                     checkboxGroupInput(inputId = "plot.options3d",
+                                        label = h3(params$plot.options.input.label),
+                                        choices = params$plot.options3d,
+                                        selected = params$plot.options3d.input.default),
+                     uiOutput(outputId = "manual.exprmin3d.input"),
+                     uiOutput(outputId = "manual.exprmax3d.input"),
                      numericInput(inputId = "span3d",
                                   label = h3(params$smoothing.span.input.label),
                                   min = params$smoothing.span.input.min,