Merge pull request #7 from majpark21/master

Update file names for download

modules/auxfunc.R

@@ -66,12 +66,12 @@ COLNTRAJ = "nCells"
 
 # file names
 FCSVOUTLIERS = 'outliers.csv'
-FCSVTCCLEAN  = 'tCoursesSelected_clean.csv'
+FCSVTCCLEAN  = 'tCoursesProcessed.csv'
 FPDFTCMEAN   = "tCoursesMeans.pdf"
 FPDFTCSINGLE = "tCourses.pdf"
 FPDFTCPSD    = 'tCoursesPsd.pdf'
-FPDFBOXAUC   = 'boxplotAUC.pdf'
-FPDFBOXTP    = 'boxplotTP.pdf'
+FPDFBOXAUC   = 'distributionAUC.pdf'
+FPDFBOXTP    = 'distributionTP.pdf'
 FPDFSCATTER  = 'scatter.pdf'
 
 # Colour definitions ----

modules/downPlot.R

@@ -36,7 +36,7 @@ downPlotUI <- function(id, label = "Download Plot") {
                  numericInput(
                    ns('inPlotWidth'),
                    "Width [in]",
-                   8.5,
+                   11,
                    min = 1,
                    width = 100
                    )
@@ -48,7 +48,7 @@ downPlotUI <- function(id, label = "Download Plot") {
                  numericInput(
                    ns('inPlotHeight'),
                    "Height [in]",
-                   11,
+                   8.5,
                    min = 1,
                    width = 100
                  )

modules/tabAUC.R

@@ -88,7 +88,7 @@ tabAUCplot = function(input, output, session, in.data, in.fname) {
              in.data = AUCcells,
              in.meascol = 'AUC',
              in.bycols = COLGR,
-             in.fname = 'data4boxplotAUC.csv')
+             in.fname = 'individualsAUC.csv')
   
   callModule(modAUCplot, 'aucPlot', 
              in.data = AUCcells, 

modules/tabClHierSpar.R

@@ -447,7 +447,7 @@ clustHierSpar <- function(input, output, session,
   output$downCellClSpar <- downloadHandler(
     filename = function() {
       paste0('clust_hierchSpar_data_',
-             input$selectPlotHierSparDiss,
+             ifelse(input$selectPlotHierSparDiss == "squared.distance", "euclidean", "manhattan"),
              '_',
              input$selectPlotHierSparLinkage, '.csv')
     },
@@ -574,7 +574,7 @@ clustHierSpar <- function(input, output, session,
   createFnameHeatMap = reactive({
     
     paste0('clust_hierchSparse_heatMap_',
-           input$selectPlotHierSparDiss,
+           ifelse(input$selectPlotHierSparDiss == "squared.distance", "euclidean", "manhattan"),
            '_',
            input$selectPlotHierSparLinkage,
            '.png')
@@ -583,7 +583,7 @@ clustHierSpar <- function(input, output, session,
   createFnameTrajPlot = reactive({
     
     paste0('clust_hierchSparse_tCourses_',
-           input$selectPlotHierSparDiss,
+           ifelse(input$selectPlotHierSparDiss == "squared.distance", "euclidean", "manhattan"),
            '_',
            input$selectPlotHierSparLinkage, 
            '.pdf')
@@ -592,7 +592,7 @@ clustHierSpar <- function(input, output, session,
   createFnameRibbonPlot = reactive({
     
     paste0('clust_hierchSparse_tCoursesMeans_',
-           input$selectPlotHierSparDiss,
+           ifelse(input$selectPlotHierSparDiss == "squared.distance", "euclidean", "manhattan"),
            '_',
            input$selectPlotHierSparLinkage, 
            '.pdf')
@@ -601,7 +601,7 @@ clustHierSpar <- function(input, output, session,
   createFnamePsdPlot = reactive({
     
     paste0('clust_hierchSparse_tCoursesPsd_',
-           input$selectPlotHierSparDiss,
+           ifelse(input$selectPlotHierSparDiss == "squared.distance", "euclidean", "manhattan"),
            '_',
            input$selectPlotHierSparLinkage, 
            '.pdf')
@@ -610,7 +610,7 @@ clustHierSpar <- function(input, output, session,
   createFnameDistPlot = reactive({
     
     paste0('clust_hierchSparse_clDist_',
-           input$selectPlotHierSparDiss,
+           ifelse(input$selectPlotHierSparDiss == "squared.distance", "euclidean", "manhattan"),
            '_',
            input$selectPlotHierSparLinkage, '.pdf')  })
   

modules/tabDist.R

@@ -37,7 +37,7 @@ tabDistPlot = function(input, output, session, in.data, in.fname) {
              in.data = data4boxPlot,
              in.meascol = 'y',
              in.bycols = c(COLRT, COLGR),
-             in.fname = 'data4boxplotTP.csv')
+             in.fname = 'individualsTP.csv')
   
   callModule(modDistPlot, 'distPlot', 
              in.data = data4boxPlot, 

modules/tabScatter.R

@@ -27,7 +27,7 @@ helpText.tabScatter = c(
   chBregression = 'Add a line with linear regression and regions of 95% confidence interval.',
   inAvgWin = paste0(
     "Length of the averaging window to smooth data before plotting. ",
-    "Useful to avoid artefacts in due to spurious variations at specific time points."
+    "Useful to avoid artefacts due to spurious variations at specific time points."
   ),
   inPlotHeight = 'Height in pixels of the displayed plot',
   inPlotNcolFacet = 'Number of facets in a row. Each facet displayes a scatter plot for a single group.',