Added CohortDiagnostics output for Breast Cancer work

CohortDiagnosticsBreastCancer/DiagnosticsExplorer.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX

CohortDiagnosticsBreastCancer/R/DisplayFunctions.R

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+camelCaseToSnakeCase <- function(string) {
+  string <- gsub("([A-Z])", "_\\1", string)
+  string <- tolower(string)
+  string <- gsub("([a-z])([0-9])", "\\1_\\2", string)
+  return(string)
+}
+
+
+camelCaseToTitleCase <- function(string) {
+  string <- gsub("([A-Z])", " \\1", string)
+  string <- gsub("([a-z])([0-9])", "\\1 \\2", string)
+  substr(string, 1, 1) <- toupper(substr(string, 1, 1))
+  return(string)
+}
+
+
+truncateStringDef <- function(columns, maxChars) {
+  list(
+    targets = columns,
+    render = DT::JS(sprintf("function(data, type, row, meta) {\n
+      return type === 'display' && data != null && data.length > %s ?\n
+        '<span title=\"' + data + '\">' + data.substr(0, %s) + '...</span>' : data;\n
+     }", maxChars, maxChars))
+  )
+}
+
+minCellCountDef <- function(columns) {
+  list(
+    targets = columns,
+    render = DT::JS("function(data, type) {
+    if (type !== 'display' || isNaN(parseFloat(data))) return data;
+    if (data >= 0) return data.toString().replace(/(\\d)(?=(\\d{3})+(?!\\d))/g, '$1,');
+    return '<' + Math.abs(data).toString().replace(/(\\d)(?=(\\d{3})+(?!\\d))/g, '$1,');
+  }")
+  )
+}
+
+minCellPercentDef <- function(columns) {
+  list(
+    targets = columns,
+    render = DT::JS("function(data, type) {
+    if (type !== 'display' || isNaN(parseFloat(data))) return data;
+    if (data >= 0) return (100 * data).toFixed(1).replace(/(\\d)(?=(\\d{3})+(?!\\d))/g, '$1,') + '%';
+    return '<' + Math.abs(100 * data).toFixed(1).replace(/(\\d)(?=(\\d{3})+(?!\\d))/g, '$1,') + '%';
+  }")
+  )
+}
+
+minCellRealDef <- function(columns, digits = 1) {
+  list(
+    targets = columns,
+    render = DT::JS(sprintf("function(data, type) {
+    if (type !== 'display' || isNaN(parseFloat(data))) return data;
+    if (data >= 0) return data.toFixed(%s).replace(/(\\d)(?=(\\d{3})+(?!\\d))/g, '$1,');
+    return '<' + Math.abs(data).toFixed(%s).replace(/(\\d)(?=(\\d{3})+(?!\\d))/g, '$1,');
+  }", digits, digits))
+  )
+}
+
+styleAbsColorBar <- function(maxValue, colorPositive, colorNegative, angle = 90) {
+  DT::JS(sprintf("isNaN(parseFloat(value))? '' : 'linear-gradient(%fdeg, transparent ' + (%f - Math.abs(value))/%f * 100 + '%%, ' + (value > 0 ? '%s ' : '%s ') + (%f - Math.abs(value))/%f * 100 + '%%)'", 
+                 angle, maxValue, maxValue, colorPositive, colorNegative, maxValue, maxValue))
+}
+
+sumCounts <- function(counts) {
+  result <- sum(abs(counts))
+  if (any(counts < 0)) {
+    return(-result)
+  } else {
+    return(result)
+  }
+
+}