added: rotated x-axis labels

README.md

@@ -40,15 +40,19 @@ install.packages(c("shiny", "shinyjs",
 ```
 
 **Note**
-As of July 2018, *sparcl* has been removed from CRAN. If you don't need sparse hierarchical clustering, you can simply comment the line `library(sparcl)` in `server.R` file or install it from the [archive](https://cran.r-project.org/web/packages/sparcl/index.html).
+As of July 2018, *sparcl* has been removed from CRAN. If you don't need sparse hierarchical clustering, you can simply comment the line `library(sparcl)` in `server.R` file or install it from the [archive](https://cran.r-project.org/web/packages/sparcl/index.html):
 
-**Additionally**, a time series analysis package need to be installed from [GitHub](https://github.com/dmattek/tca-package):
+```
+install_url('https://cran.r-project.org/src/contrib/Archive/sparcl/sparcl_1.0.3.tar.gz')
+```
+
+**Additionally**, a time series analysis package needs to be installed from [GitHub](https://github.com/dmattek/tca-package):
 
 ```
 install_github("dmattek/tca-package")
 ```
 
-The `install_github` function is available in *devtools* package:
+The `install_url` and `install_github` functions are available in *devtools* package:
 
 ```
 install.packages("devtools")

modules/auxfunc.R

@@ -170,6 +170,22 @@ getClCol <- function(in.dend, in.k) {
 #####
 ## Common plotting functions
 
+# Build Function to Return Element Text Object
+# From: https://stackoverflow.com/a/36979201/1898713
+rotatedAxisElementText = function(angle, position='x', size = 12){
+  angle     = angle[1]; 
+  position  = position[1]
+  positions = list(x=0, y=90, top=180, right=270)
+  if(!position %in% names(positions))
+    stop(sprintf("'position' must be one of [%s]",paste(names(positions),collapse=", ")), call.=FALSE)
+  if(!is.numeric(angle))
+    stop("'angle' must be numeric",call.=FALSE)
+  rads = (-angle - positions[[ position ]])*pi/180
+  hjust = round((1 - sin(rads)))/2
+  vjust = round((1 + cos(rads)))/2
+  element_text(size = 12, angle = angle, vjust = vjust, hjust = hjust)
+}
+
 myGgplotTheme = 
   theme_bw(base_size = 8, base_family = "Helvetica") +
   theme(

modules/boxPlot.R

@@ -31,7 +31,6 @@ modBoxPlotUI =  function(id, label = "Plot Box-plots") {
           ),
           selected = 'top'
         ),
-        checkboxInput(ns('chBxAxisLabelsRotate'), 'Rotate x-axis labels?'),
         uiOutput(ns('uiPlotBoxNotches')),
         uiOutput(ns('uiPlotBoxOutliers')),
         uiOutput(ns('uiPlotBoxDodge')),
@@ -56,7 +55,11 @@ modBoxPlotUI =  function(id, label = "Plot Box-plots") {
           min = 100,
           width = '100px',
           step = 50
-        )
+        ),
+        radioButtons(ns("rBAxisLabelsRotate"), "X-axis labels:",
+                     c("horizontal" = 0,
+                       "45deg" = 45,
+                       "90 deg" = 90))
       )
     ),
     
@@ -238,15 +241,9 @@ modBoxPlot = function(input, output, session,
       ylab('') +
       ggplotTheme() + 
       #myGgplotTheme + 
-      theme(legend.position = input$selPlotBoxLegendPos)
-    
-    if (input$chBxAxisLabelsRotate)
-      p.out = p.out +
-      theme(axis.text.x = element_text(size = 12, angle = 45, hjust = 1))
-    else
-      p.out = p.out +
-      theme(axis.text.x = element_text(size = 12))
-    
+      theme(legend.position = input$selPlotBoxLegendPos,
+            axis.text.x = element_text(size = 12, angle = as.numeric(input$rBAxisLabelsRotate), hjust = ifelse(input$rBAxisLabelsRotate == 0, 0, 1)))
+
     
     return(p.out)
   }

modules/clDistPlot.R

@@ -2,6 +2,10 @@ modClDistPlotUI =  function(id, label = "Plot Fractions WIthin Clusters") {
   ns <- NS(id)
   
   tagList(
+    radioButtons(ns("rBAxisLabelsRotate"), "X-axis labels:",
+                 c("horizontal" = 0,
+                   "45deg" = 45,
+                   "90 deg" = 90)),
     actionButton(ns('butPlotClDist'), 'Plot!'),
     plotOutput(ns('outPlotClDist'), height = '800px', width = 'auto'),
     downPlotUI(ns('downPlotClDist'), "Download PDF")
@@ -45,11 +49,18 @@ modClDistPlot = function(input, output, session, in.data, in.cols = NULL, in.fna
                                         #limits = in.cols()$cl.no)
     
     
+    loc.rads = as.numeric(input$rBAxisLabelsRotate) * pi / 180
+    loc.hjust = 0.5*(1-sin(loc.rads))
+    loc.vjust = 0.5*(1-cos(loc.rads))
+    
     p.out = p.out + 
       scale_y_continuous(labels = percent) +
       ylab("percentage of cells\n") +  
       xlab("") +  
-      ggplotTheme()
+      ggplotTheme() +
+      theme(
+        axis.text.x = rotatedAxisElementText(as.numeric(input$rBAxisLabelsRotate))
+    )
       #myGgplotTheme
     
     return(p.out)

server.R

@@ -18,7 +18,7 @@ library(dendextend) # for color_branches
 library(colorspace) # for palettes (used to colour dendrogram)
 library(RColorBrewer)
 # sparcl temporarily unavailable on CRAN
-#library(sparcl) # sparse hierarchical and k-means
+library(sparcl) # sparse hierarchical and k-means
 library(scales) # for percentages on y scale
 library(dtw) # for dynamic time warping
 library(imputeTS) # for interpolating NAs

ui.R

@@ -142,13 +142,13 @@ shinyUI(fluidPage(
         tabPanel(
           'Hierarchical',
           clustHierUI('tabClHier')
-        )
+        ),
         
         # sparse hierarchical clustering package sparcl temporarily unavailable from CRAN
-        # tabPanel(
-        #   'Hierarchical Sparse',
-        #   clustHierSparUI('tabClHierSpar')
-        #)
+         tabPanel(
+           'Hierarchical Sparse',
+           clustHierSparUI('tabClHierSpar')
+        )
       ))
   )
 ))
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