From 27cb2bb37939370cc732df8e15fe9dadc0a38b83 Mon Sep 17 00:00:00 2001
From: Thomas Brooks <thobr@sas.upenn.edu>
Date: Wed, 26 Jun 2019 14:26:53 -0400
Subject: [PATCH 01/16] Enable error modal for sharing

---
 templates/spreadsheets/comparison.html | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/templates/spreadsheets/comparison.html b/templates/spreadsheets/comparison.html
index 18cf03d..7048a1b 100644
--- a/templates/spreadsheets/comparison.html
+++ b/templates/spreadsheets/comparison.html
@@ -12,6 +12,9 @@
     PCA_HEIGHT = 800;
     PCA_SYMBOL = "M 0,-15 A 15,15 0 0,1 15,0 L 0,0 Z M 15,0 A 15,15 0 0,1 -15,0 A 15,15 0 0,1 0,-15 L 0,-10 A 10,10 0 0,0 -10,0 A 10,10 0 0,0 10,0";
     $(document).ready(function () {
+        // Handles to the error-handling modal
+        nitecap_error = $("#error-modal");
+        nitecap_error_message = $("#error-modal-message")
 
         spreadsheet_ids = {{ spreadsheet_ids | safe }};
 

From 42ec7663e7af12f667c413146558f56740b47a31 Mon Sep 17 00:00:00 2001
From: Thomas Brooks <thobr@sas.upenn.edu>
Date: Wed, 26 Jun 2019 14:38:56 -0400
Subject: [PATCH 02/16] Display error modals on Ajax failures

---
 templates/spreadsheets/comparison.html | 15 ++++++++++++---
 1 file changed, 12 insertions(+), 3 deletions(-)

diff --git a/templates/spreadsheets/comparison.html b/templates/spreadsheets/comparison.html
index 7048a1b..b2cae61 100644
--- a/templates/spreadsheets/comparison.html
+++ b/templates/spreadsheets/comparison.html
@@ -30,6 +30,9 @@
             error: function(error) {
                 console.log("Error loading spreadsheets");
                 console.log(error);
+
+                nitecap_error_message.text("Error loading spreadsheets");
+                nitecap_error.modal();
             }
         });
 
@@ -104,6 +107,9 @@
             error: function(error) {
                 console.log("Error loading JTK values");
                 console.log(error);
+
+                nitecap_error_message.text("Error loading JTK values");
+                nitecap_error.modal();
             }
         });
 
@@ -143,7 +149,9 @@
                 error: function(error) {
                     console.log("Error loading upside values");
                     console.log(error);
-                    response = error.responseText;
+
+                    nitecap_error_message.text("Error loading comparison statistics");
+                    nitecap_error.modal();
                 }
             });
         }
@@ -1311,8 +1319,9 @@ <h5 class="modal-title text-white">SHARE this spreadsheet</h5>
                     error: function (error) {
                         console.log("Error running PCA");
                         console.log(error);
-                        alert.text(error.responseText);
-                        alert.show();
+
+                        nitecap_error_message.text("Error running PCA");
+                        nitecap_error.modal();
                     },
                     complete: function() {
                         vm.pca.running = false;

From da103c4b46b3d91c6d729fb1bb7e3809c0108b13 Mon Sep 17 00:00:00 2001
From: Thomas Brooks <thobr@sas.upenn.edu>
Date: Wed, 26 Jun 2019 14:58:43 -0400
Subject: [PATCH 03/16] Handle null q-values in sorting rows

---
 templates/spreadsheets/comparison.html | 28 +++++++++++++++++++++-----
 1 file changed, 23 insertions(+), 5 deletions(-)

diff --git a/templates/spreadsheets/comparison.html b/templates/spreadsheets/comparison.html
index b2cae61..29bdcc6 100644
--- a/templates/spreadsheets/comparison.html
+++ b/templates/spreadsheets/comparison.html
@@ -583,7 +583,8 @@ <h5 class="modal-title text-white">SHARE this spreadsheet</h5>
           description: "Nitecap significance of rhythmicity for primary dataset.",
          per_spreadsheet: true,
          num_spreadsheets:'any',
-         sort_value:'tds'},
+         sort_value:'tds',
+         secondary_sort_value:'qs'},
         {name: "JTK",
          value: {p: "jtk_ps",
                  q: "jtk_qs"},
@@ -1415,16 +1416,29 @@ <h5 class="modal-title text-white">SHARE this spreadsheet</h5>
             },
 
             sort_function: function () {
+                // We sort by the value specified in sort_by
+                // We also have a 'secondary sort value' which is used purely as a null/not-null check
+                // So if secondary sort value is null then we will sort the value to the end as if the main value were null
+                // This solves the problem where q-values are null and being sorted to the front of the list particulary
+                // from filters re-running q-values (which nulls them if filtered) and then being viewed without that filter
                 let vm = this;
                 let sorter = null;
                 let value = null;
+                let secondary_value = null;
 
                 if (this.sort_by.stat.sort_value !== undefined) {
                     value = this.sort_by.stat.sort_value;
+                    if (this.sort_by.stat.secondary_sort_value !== undefined) {
+                        secondary_value = this.sort_by.stat.secondary_sort_value;
+                    } else {
+                        secondary_value = value;
+                    }
                 } else if (typeof this.sort_by.stat.value === 'string') {
                     value = this.sort_by.stat.value;
+                    secondary_value = value;
                 } else {
                     value = this.sort_by.stat.value.p;
+                    secondary_value = this.sort_by.stat.value.q;
                 }
 
                 let sort_direction = 1;
@@ -1434,16 +1448,20 @@ <h5 class="modal-title text-white">SHARE this spreadsheet</h5>
 
                 if (vm.sort_by.spreadsheet_num !== undefined) {
                     sorter = function (i,j) {
-                        let a = vm.spreadsheets[vm.sort_by.spreadsheet_num][value][i];
-                        let b = vm.spreadsheets[vm.sort_by.spreadsheet_num][value][j];
+                        let a = vm.spreadsheets[vm.sort_by.spreadsheet_num][secondary_value][i] &&
+                                    vm.spreadsheets[vm.sort_by.spreadsheet_num][value][i];
+                        let b = vm.spreadsheets[vm.sort_by.spreadsheet_num][secondary_value][j] &&
+                                    vm.spreadsheets[vm.sort_by.spreadsheet_num][value][j];
                         return compare(a ? a * sort_direction : a, // multiply by +/- 1 but not if null
                                        b ? b * sort_direction : b,
                                        i, j);
                     };
                 } else {
                     sorter = function (i,j) {
-                        let a = vm.stats[value][i];
-                        let b = vm.stats[value][j];
+                        let a = vm.stats[secondary_value][i]
+                                    && vm.stats[value][i];
+                        let b = vm.stats[secondary_value][j]
+                                    && vm.stats[value][j];
                         return compare(a ? a * sort_direction : b, // multiply by +/- 1 but not if null
                                        b ? b * sort_direction : b,
                                        i, j);

From fbbf4660ead9c6dac96cf5226cf0dbfaeaf0255b Mon Sep 17 00:00:00 2001
From: Thomas Brooks <thobr@sas.upenn.edu>
Date: Mon, 1 Jul 2019 10:41:40 -0400
Subject: [PATCH 04/16] Make stats look clickable

---
 static/css/main.css                    | 4 ++++
 templates/spreadsheets/comparison.html | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/static/css/main.css b/static/css/main.css
index c6cc27c..3a46653 100644
--- a/static/css/main.css
+++ b/static/css/main.css
@@ -194,6 +194,10 @@ body {
     color: #FFF;
 }
 
+.stats-box td {
+    cursor: pointer;
+}
+
 #spreadsheetTable.dataTable tr.selected td.select-checkbox::after, #spreadsheetTable.dataTable tr.selected th.select-checkbox::after {
     font-family: "Font Awesome 5 Free";
     content: "\f14a";
diff --git a/templates/spreadsheets/comparison.html b/templates/spreadsheets/comparison.html
index 29bdcc6..c7fdf78 100644
--- a/templates/spreadsheets/comparison.html
+++ b/templates/spreadsheets/comparison.html
@@ -303,7 +303,7 @@ <h1>Spreadsheet Viewer</h1>
                                 <th scope="col">Secondary</th>
                             </tr>
                         </thead>
-                        <tbody v-if="spreadsheets !== null">
+                        <tbody v-if="spreadsheets !== null" class="stats-box">
                             <template v-for="stat in useable_stats">
                                 <tr>
                                     <td v-bind:rowspan="typeof stat.value === 'string' ? 1 : 2">

From 88eee2ff1054dcc2e513c6e65ed092364ba35978 Mon Sep 17 00:00:00 2001
From: Thomas Brooks <thobr@sas.upenn.edu>
Date: Mon, 1 Jul 2019 10:42:22 -0400
Subject: [PATCH 05/16] Update q-values in statsbox as sort changing

---
 templates/spreadsheets/comparison.html | 22 +++++++++++++++++++++-
 1 file changed, 21 insertions(+), 1 deletion(-)

diff --git a/templates/spreadsheets/comparison.html b/templates/spreadsheets/comparison.html
index c7fdf78..15d1992 100644
--- a/templates/spreadsheets/comparison.html
+++ b/templates/spreadsheets/comparison.html
@@ -231,7 +231,7 @@ <h1>Spreadsheet Viewer</h1>
                     <row-selector v-bind:sort-order="sort_order"
                                   v-bind:filtered="filtered"
                                   v-bind:num-rows="21"
-                                  v-bind:q-values="spreadsheets[0] ? spreadsheets[0].qs : []"
+                                  v-bind:q-values="label_qs"
                                   v-bind:selected-row="selected_row"
                                   v-bind:labels="labels"
                                   v-bind:label-max-length="35"
@@ -1487,6 +1487,26 @@ <h5 class="modal-title text-white">SHARE this spreadsheet</h5>
                 return sort_order;
             },
 
+            label_qs: function () {
+                let value = this.sort_by.stat.value;
+
+                if (typeof value === 'string') {
+                    // No inherent q-value for this sort value
+                    // we default to Nitecap of primary spreadsheet
+                    return this.spreadsheets[0] ? this.spreadsheets[0].ps : [];
+                }
+
+                if (this.sort_by.spreadsheet_num !== undefined) {
+                    let sp = this.spreadsheets[this.sort_by.spreadsheet_num];
+                    let vq = value.q;
+                    let vals = sp ? sp[vq]: [];
+                    return vals;
+                    return this.spreadsheets[this.sort_by.spreadsheet_num][value.q];
+                } else {
+                    return this.stats[value.q];
+                }
+            },
+
             filtered: function () {
                 let vm = this;
                 let filtered_out = this.labels.map( function (x) {return false;} );

From df7ff73af06e6cd90dd0d18775bdc9c18b430ff0 Mon Sep 17 00:00:00 2001
From: Thomas Brooks <thobr@sas.upenn.edu>
Date: Mon, 1 Jul 2019 11:34:22 -0400
Subject: [PATCH 06/16] Fix multi-cycle comparisons (again)

---
 models/spreadsheets/views.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/models/spreadsheets/views.py b/models/spreadsheets/views.py
index 6828ea1..6e177d8 100644
--- a/models/spreadsheets/views.py
+++ b/models/spreadsheets/views.py
@@ -738,7 +738,7 @@ def get_upside():
 
                 dfs, combined_index = Spreadsheet.join_spreadsheets(spreadsheets)
 
-                datasets = [df[spreadsheet.get_data_columns()].values for df, spreadsheet in zip(dfs, spreadsheets)]
+                datasets = [df[spreadsheet.get_data_columns(by_day=False)].values for df, spreadsheet in zip(dfs, spreadsheets)]
 
             # Run the actual upside calculation
             upside_p = nitecap.upside.main(spreadsheets[primary].num_replicates_by_time, datasets[primary],

From 11d7e1146916c17be67d80cedad72fbfb759d49c Mon Sep 17 00:00:00 2001
From: Thomas Brooks <thobr@sas.upenn.edu>
Date: Mon, 1 Jul 2019 11:47:58 -0400
Subject: [PATCH 07/16] Force reloading of main.css and main.js

---
 templates/base.html | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/templates/base.html b/templates/base.html
index 40f0de7..d348154 100644
--- a/templates/base.html
+++ b/templates/base.html
@@ -21,7 +21,7 @@
     <link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css" />
     <link rel="stylesheet" href="https://cdn.datatables.net/select/1.3.0/css/select.dataTables.min.css" />
     <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/jqueryui/1.12.1/jquery-ui.css" />
-    <link rel="stylesheet" href="{{ url_for('static', filename='css/main.css') }}?v=2" />
+    <link rel="stylesheet" href="{{ url_for('static', filename='css/main.css') }}?v=3" />
     <link rel="icon" type="image/png" sizes="32x32" href="{{ url_for('static', filename='images/favicon-32x32.png') }}">
     <link rel="icon" type="image/png" sizes="16x16" href="{{ url_for('static', filename='images/favicon-16x16.png') }}">
     <link rel="shortcut icon" href="{{ url_for('static', filename='images/favicon.ico') }}">
@@ -35,7 +35,7 @@
     <script src="https://cdn.plot.ly/plotly-latest.min.js"></script>
     <script src="https://cdnjs.cloudflare.com/ajax/libs/mustache.js/3.0.1/mustache.min.js"></script>
     <script src="{{ url_for('static', filename='js/moment.js') }}"></script>
-    <script src="{{ url_for('static', filename='js/main.js') }}?v=3"></script>
+    <script src="{{ url_for('static', filename='js/main.js') }}?v=4"></script>
 </head>
 <body>
 <div class="container">

From da9e4b94d07c055bfa22753e7ba184aeb309262d Mon Sep 17 00:00:00 2001
From: Thomas Brooks <thobr@sas.upenn.edu>
Date: Wed, 3 Jul 2019 12:22:21 -0400
Subject: [PATCH 08/16] Fix mean + max value filters on single spreadsheets

---
 static/js/main.js                      | 55 ++++++++++++++++++++++++++
 templates/spreadsheets/comparison.html | 25 ++++++++----
 2 files changed, 72 insertions(+), 8 deletions(-)

diff --git a/static/js/main.js b/static/js/main.js
index 09c56f4..4abb2e7 100644
--- a/static/js/main.js
+++ b/static/js/main.js
@@ -230,6 +230,61 @@ function means(table) {
     return table.map(mean);
 }
 
+// Util that takes a two-dim array-of-arrays and computes the sum of each row
+// NaNs are skipped (if all are NaN, then NaN is returned)
+// If axis=1,  then sums on each row in the table, ie does sum(table[i][j])  summing over j
+// If axis=0, then sums on the first axis, i.e. does sum(table[i][j]) summing over i
+function sums(table, axis) {
+    axis = axis !== undefined ? axis : 1;
+
+    function sum(row) {
+        let sum = 0;
+        let count = 0;
+        row.forEach( function(x) {
+            if (isNaN(x) || x === null) {
+                return;
+            }
+            sum += x;
+            count += 1;
+        } );
+
+        if (count === 0) {
+            return NaN;
+        }
+        return sum;
+    };
+
+    if (axis === 1) {
+        // Take the sum of data[i][*]
+        return table.map(sum);
+    } else if (axis === 0) {
+        // Select out data[*][j] and take the sum
+        return table[0].map( function (_,j) {
+            return sum(table.map( function(row) {
+                return row[j];
+            }));
+        });
+    } else {
+        return "axis must be 1 (default) or 0";
+    }
+}
+
+// Util that takes a two-dim array-of-arrays and computes the number of non-NaN elements
+// in each row
+function numValids(table) {
+    function count(row) {
+        let count = 0;
+        row.forEach( function(x) {
+            if( isNaN(x) || x === null ){
+                return;
+            }
+            count += 1;
+        });
+        return count;
+    }
+    return table.map(count);
+}
+
 // Util to pad a string with copies of a character
 function padEnd(string, length, character) {
     if (string.length > length) {
diff --git a/templates/spreadsheets/comparison.html b/templates/spreadsheets/comparison.html
index 15d1992..cb7face 100644
--- a/templates/spreadsheets/comparison.html
+++ b/templates/spreadsheets/comparison.html
@@ -641,7 +641,7 @@ <h5 class="modal-title text-white">SHARE this spreadsheet</h5>
                                 return maximums(spreadsheet.data);
                          });
                          return maxes[0].map( function(row, i) {
-                            return Math.max(maxes[0][i], maxes[1][i]);
+                            return Math.max.apply(null, maxes.map(function(max){return max[i];}));
                         });
                     },
                 name: "Maximum value",
@@ -649,15 +649,24 @@ <h5 class="modal-title text-white">SHARE this spreadsheet</h5>
                 key:"max_value"},
         {values: function () {
                     // Grand means across both datasets within each row
-                    // TODO: better support for missing values (different numbers missing in each spreadsheet)
-                    let means = app.spreadsheets.map(function (spreadsheet) {
-                        return means(spreadsheet.data);
+                    // skipping over NaN/null values
+                    let sums_ = app.spreadsheets.map(function(spreadsheet) {
+                        let summed_rows = sums(spreadsheet.data);
+                        return summed_rows;
                     });
-                    let a = app.spreadsheets[0].data[0].length;
-                    let b = app.spreadsheets[1].data[0].length;
-                    return means[0].map( function(row, i) {
-                        return (means[0][i]*a + means[1][i]*b) / (a + b);
+                    let total_sums = sums(sums_, 0);
+
+                    let nonnans = app.spreadsheets.map(function(spreadsheet) {
+                        return numValids(spreadsheet.data);
+                    });
+                    let total_nonnans = sums(nonnans, 0);
+
+                    let divide = function(a,b) { return a/b; };
+
+                    let means = total_sums.map(function(sum, i) {
+                        return sum / total_nonnans[i];
                     });
+                    return means;
                 },
                 name: "Mean value",
                 independent: true,

From 3dace26c80b608bc5e62287326ffe74a0f0c0c51 Mon Sep 17 00:00:00 2001
From: Thomas Brooks <thobr@sas.upenn.edu>
Date: Wed, 3 Jul 2019 12:30:46 -0400
Subject: [PATCH 09/16] Force refresh of main.js

---
 templates/base.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/templates/base.html b/templates/base.html
index d348154..f70d3b8 100644
--- a/templates/base.html
+++ b/templates/base.html
@@ -35,7 +35,7 @@
     <script src="https://cdn.plot.ly/plotly-latest.min.js"></script>
     <script src="https://cdnjs.cloudflare.com/ajax/libs/mustache.js/3.0.1/mustache.min.js"></script>
     <script src="{{ url_for('static', filename='js/moment.js') }}"></script>
-    <script src="{{ url_for('static', filename='js/main.js') }}?v=4"></script>
+    <script src="{{ url_for('static', filename='js/main.js') }}?v=5"></script>
 </head>
 <body>
 <div class="container">

From c5fabe335ee638dd312f44c33baa8f57adbbe0ef Mon Sep 17 00:00:00 2001
From: Thomas Brooks <thobr@sas.upenn.edu>
Date: Wed, 3 Jul 2019 12:42:45 -0400
Subject: [PATCH 10/16] Fixed SEM error bars

Forgot a square root
---
 static/js/main.js   | 2 +-
 templates/base.html | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/static/js/main.js b/static/js/main.js
index 4abb2e7..95f11a1 100644
--- a/static/js/main.js
+++ b/static/js/main.js
@@ -183,7 +183,7 @@ function rowStatsByTimepoint(row, times) {
     });
 
     var stds = variances.map(Math.sqrt);
-    var sems = stds.map(function (std, time) { return std / reps_per_timepoint[time]; });
+    var sems = stds.map(function (std, time) { return std / Math.sqrt(reps_per_timepoint[time]); });
 
     return {means: means, variances: variances, stds: stds,  sems:sems};
 }
diff --git a/templates/base.html b/templates/base.html
index f70d3b8..60cfdcc 100644
--- a/templates/base.html
+++ b/templates/base.html
@@ -35,7 +35,7 @@
     <script src="https://cdn.plot.ly/plotly-latest.min.js"></script>
     <script src="https://cdnjs.cloudflare.com/ajax/libs/mustache.js/3.0.1/mustache.min.js"></script>
     <script src="{{ url_for('static', filename='js/moment.js') }}"></script>
-    <script src="{{ url_for('static', filename='js/main.js') }}?v=5"></script>
+    <script src="{{ url_for('static', filename='js/main.js') }}?v=6"></script>
 </head>
 <body>
 <div class="container">

From 98b382d700df5bdacc886a3430551bead5cdb7a0 Mon Sep 17 00:00:00 2001
From: Thomas Brooks <thobr@sas.upenn.edu>
Date: Wed, 3 Jul 2019 12:43:16 -0400
Subject: [PATCH 11/16] Allow points + std/sem plot styles

---
 templates/spreadsheets/comparison.html | 28 ++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/templates/spreadsheets/comparison.html b/templates/spreadsheets/comparison.html
index cb7face..1a417f8 100644
--- a/templates/spreadsheets/comparison.html
+++ b/templates/spreadsheets/comparison.html
@@ -259,7 +259,9 @@ <h1>Spreadsheet Viewer</h1>
                         <option value="mean">Mean only</option>
                         <option value="mean_points">Points and Mean</option>
                         <option value="std">Standard Deviations</option>
+                        <option value="std_points">Standard Deviations and Points</option>
                         <option value="SEM">SEM</option>
+                        <option value="SEM_points">SEM and Points</option>
                     </select>
                 </div>
                 <div class="form-inline">
@@ -888,11 +890,37 @@ <h5 class="modal-title text-white">SHARE this spreadsheet</h5>
                         trace.x = stats.means.map( function (x,i) {return i;} ); // Just 0,1,2,3...
                         trace.y = stats.means;
                         trace.error_y = {type: 'data', array:stats.stds, visible:true};
+                    } else if (plot_style === "std_points") {
+                        trace.mode = "lines";
+                        trace.x = stats.means.map( function (x,i) {return i;} ); // Just 0,1,2,3...
+                        trace.y = stats.means;
+                        trace.error_y = {type: 'data', array:stats.stds, visible:true};
+                        traces.push({
+                            x: plot_x_values,
+                            y: raw_y_values,
+                            showlegend: false,
+                            type: 'scatter',
+                            mode: 'markers',
+                            marker: {color: spreadsheet_color},
+                        });
                     } else if (plot_style === "SEM") {
                         trace.mode = "lines";
                         trace.x = stats.means.map( function (x,i) {return i;} ); // Just 0,1,2,3...
                         trace.y = stats.means;
                         trace.error_y = {type: 'data', array:stats.sems, visible:true};
+                    } else if (plot_style === "SEM_points") {
+                        trace.mode = "lines";
+                        trace.x = stats.means.map( function (x,i) {return i;} ); // Just 0,1,2,3...
+                        trace.y = stats.means;
+                        trace.error_y = {type: 'data', array:stats.sems, visible:true};
+                        traces.push({
+                            x: plot_x_values,
+                            y: raw_y_values,
+                            type: 'scatter',
+                            showlegend: false,
+                            mode: 'markers',
+                            marker: {color: spreadsheet_color},
+                        });
                     }
 
                     traces.push(trace);

From 19563c7560b135fc418a70d0e8ba667a41f51489 Mon Sep 17 00:00:00 2001
From: Thomas Brooks <thobr@sas.upenn.edu>
Date: Wed, 3 Jul 2019 12:48:15 -0400
Subject: [PATCH 12/16] Move Download Plot button to correct spot

---
 templates/spreadsheets/comparison.html | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/templates/spreadsheets/comparison.html b/templates/spreadsheets/comparison.html
index 1a417f8..aa36997 100644
--- a/templates/spreadsheets/comparison.html
+++ b/templates/spreadsheets/comparison.html
@@ -244,12 +244,12 @@ <h1>Spreadsheet Viewer</h1>
                     </div>
                 </div>
             </div>
-            <div class='p-3'>
-                <button class="btn btn-primary" v-on:click="downloadPlot">Download Plot</button>
-            </div>
         </span>
         <div class='col-auto'>
             <span id="scatter_plot" style="width:625px;height:525px;vertical-align: top"></span>
+            <div class='p-3 float-right'>
+                <button class="btn btn-primary" v-on:click="downloadPlot">Download Plot</button>
+            </div>
             <form class="form-group">
                 <div class="form-inline">
                     <label for="plot_style_select">Plot style</label>

From e5eb9827e07119a2a6d1b65ef5e43ea611bc5490 Mon Sep 17 00:00:00 2001
From: Thomas Brooks <thobr@sas.upenn.edu>
Date: Wed, 3 Jul 2019 12:54:27 -0400
Subject: [PATCH 13/16] Allow re-ordering of spreadsheets

---
 templates/spreadsheets/comparison.html | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/templates/spreadsheets/comparison.html b/templates/spreadsheets/comparison.html
index aa36997..5183c0c 100644
--- a/templates/spreadsheets/comparison.html
+++ b/templates/spreadsheets/comparison.html
@@ -250,6 +250,9 @@ <h1>Spreadsheet Viewer</h1>
             <div class='p-3 float-right'>
                 <button class="btn btn-primary" v-on:click="downloadPlot">Download Plot</button>
             </div>
+            <div class='p-3 float-right'>
+                <button class="btn btn-primary btn-sm" v-on:click="shiftSpreadsheets">Reorder Spreadsheets</button>
+            </div>
             <form class="form-group">
                 <div class="form-inline">
                     <label for="plot_style_select">Plot style</label>
@@ -1417,6 +1420,14 @@ <h5 class="modal-title text-white">SHARE this spreadsheet</h5>
                 });
             },
 
+            shiftSpreadsheets: function () {
+                // Shifts through the spreadsheets in order
+                let spreadsheets = this.spreadsheets;
+                let first = spreadsheets[0];
+                let tail = spreadsheets.slice(1);
+                this.spreadsheets = tail.concat(first);
+            },
+
         },
 
         computed: {

From 81afb6d4e909d2a0d86c66a590b6cb8993f1bda0 Mon Sep 17 00:00:00 2001
From: Thomas Brooks <thobr@sas.upenn.edu>
Date: Wed, 3 Jul 2019 12:55:53 -0400
Subject: [PATCH 14/16] No reorder button if only 1 spreadsheet

---
 templates/spreadsheets/comparison.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/templates/spreadsheets/comparison.html b/templates/spreadsheets/comparison.html
index 5183c0c..add3479 100644
--- a/templates/spreadsheets/comparison.html
+++ b/templates/spreadsheets/comparison.html
@@ -251,7 +251,7 @@ <h1>Spreadsheet Viewer</h1>
                 <button class="btn btn-primary" v-on:click="downloadPlot">Download Plot</button>
             </div>
             <div class='p-3 float-right'>
-                <button class="btn btn-primary btn-sm" v-on:click="shiftSpreadsheets">Reorder Spreadsheets</button>
+                <button class="btn btn-primary btn-sm" v-on:click="shiftSpreadsheets" v-if="spreadsheets.length > 1">Reorder Spreadsheets</button>
             </div>
             <form class="form-group">
                 <div class="form-inline">

From 4c76d33efbe00c84e9707e190243307930f5a37a Mon Sep 17 00:00:00 2001
From: Thomas Brooks <thobr@sas.upenn.edu>
Date: Wed, 3 Jul 2019 13:22:32 -0400
Subject: [PATCH 15/16] Update FAQs

---
 templates/faqs.html | 20 ++++++++++++++++----
 1 file changed, 16 insertions(+), 4 deletions(-)

diff --git a/templates/faqs.html b/templates/faqs.html
index 7b26742..83c2ae6 100644
--- a/templates/faqs.html
+++ b/templates/faqs.html
@@ -41,7 +41,7 @@ <h5 class="mb-0">
                 <h5 class="mb-0">
                     <button class="btn btn-link" data-toggle="collapse" data-target="#collapseTwo"
                              aria-expanded="true" aria-controls="collapseTwo">
-                        Why are my ANOVA p-values blank?
+                        Why are my ANOVA p-values N/A?
                     </button>
                 </h5>
             </div>
@@ -70,7 +70,10 @@ <h5 class="mb-0">
                         Nitecap accepts most spreadsheets as is and supports Excel xls, xlsx spreadsheets (with your data in the first sheet in the file, if multiple sheets) as well as tab-separated and comma-separated files.
                         The data should be formatted with one column per sample and one row per one feature (e.g. gene, protein or other value measured).
                         Which column corresponds to which timepoint is set by the user after uploading the spreadsheet and no specific column headers are required.
-                        For convenience, if sample columns are labelled as ZT## or CT##  (e.g. CT0, CT4, CT8, CT12, ...) then the number values will be used to infer timepoints when possible.
+                        For convenience, if sample columns headers include ZT## or CT##  (e.g. CT0, CT4, CT8, CT12, ...) then the number values will be used to infer timepoints when possible and for labels of timepoints.
+                        Similarly, if the columns contains ##:## (e.g. 12:04) time values, then those will be used.
+                    </p>
+                    <p>
                         Additional columns are no problem and can be used to label the values by selecting ID and multiple columns may be used as ID columns.
                     </p>
                 </div>
@@ -159,10 +162,15 @@ <h5 class="mb-0">
                 <div class="card-body">
                     <p>
                         Nitecap is currently under development and has not yet been published, so no citation is yet possible.
+                        If you publish a work using Nitecap, please let <a href="mailto:thobr@sas.upenn.edu">let us know</a>.
                     </p>
                     <p>
                         If you use the JTK analysis results in your paper, the <a href="https://openwetware.org/wiki/HughesLab:JTK_Cycle">developers of JTK_cycle</a> ask users to cite <a href="http://www.ncbi.nlm.nih.gov/pubmed/20876817">their paper</a>.
                     </p>
+                    <p>
+                        If you use phase and amplitude difference statistics, you can cite Bingham, Arbogast, Cornelissen Guillaume, Lee, Halberg "Inferential Statistical Methods for Estimating and Comparing Cosinor Parameters," 1982.
+
+                    </p>
                 </div>
             </div>
         </div>
@@ -179,13 +187,17 @@ <h5 class="mb-0">
             <div id="collapseEight" class="collapse" aria-labelledby="headingEight" data-parent="#faq_list">
                 <div class="card-body">
                     <p>
-                        There is a share button on every dataset which gives a URL that can be given to your colleagues to access the dataset.
+                        If you have logged into your account, there is a share button on every dataset which gives a URL that can be given to your colleagues to access the dataset.
                         Note that anyone with the URL can access it, so consider who you share it with.
                     </p>
                     <p>
                         When someone opens the link, they receive a copy of the dataset and none of the changes they make will be reflected in your copy.
                         If you modify your dataset, then that modification will go to anyone who clicks the link after your modification, but not for anyone who clicked before.
                     </p>
+                    <p>
+                        Unfortunately we do not yet support sharing comparisons between multiple spreadsheets.
+                        Instead, you should share all the individual spreadsheets and if your colleague opens each spreadsheet link, they can perform a comparison by visiting their <a href="/spreadsheets/display_spreadsheets">spreadsheet list</a> page.
+                    </p>
                 </div>
             </div>
         </div>
@@ -214,7 +226,7 @@ <h5 class="mb-0">
                         In particular, note that if any one of the datasets has non-significant rhythmicity, the p-value for the phase test will be non-significant.
                         This is desirable since the phase of a non-rhythmic feature is undefined.
                         Hence this p-value is significant only when all are significantly rhythmic and the difference in their phases are significant.
-                        The amplitude of a non-sigificant rhythmicity should  be low and hence an amplitude difference is still meaningful and the test is more powerful.
+                        The amplitude of a non-significant rhythmicity should  be low and hence an amplitude difference is still meaningful and the test is more powerful.
                     </p>
                 </div>
             </div>

From 194c724b13a1cb183a4ed3b1ffa97d06bf73a77e Mon Sep 17 00:00:00 2001
From: Thomas Brooks <thobr@sas.upenn.edu>
Date: Mon, 8 Jul 2019 15:54:38 -0400
Subject: [PATCH 16/16] Robust to spreadsheet swaps

---
 templates/spreadsheets/comparison.html | 27 +++++++++++++-------------
 1 file changed, 13 insertions(+), 14 deletions(-)

diff --git a/templates/spreadsheets/comparison.html b/templates/spreadsheets/comparison.html
index add3479..007a21a 100644
--- a/templates/spreadsheets/comparison.html
+++ b/templates/spreadsheets/comparison.html
@@ -91,17 +91,12 @@
                 let jtk_ps = response['jtk_ps'];
                 let jtk_qs = response['jtk_qs'];
 
-                // Find the right spreadsheets and put each jtk_ps/qs into it
-                spreadsheet_ids.forEach(function(id, i) {
-                    app.spreadsheets.forEach(function(spreadsheet) {
-                        if (spreadsheet.spreadsheet_id == id) {
-                            // For Vue performance see VUE PERF NOTE
-                            Object.preventExtensions(jtk_ps[i]);
-                            Object.preventExtensions(jtk_qs[i]);
-                            spreadsheet.jtk_ps = jtk_ps[i];
-                            spreadsheet.jtk_qs = jtk_qs[i];
-                        }
-                    });
+                spreadsheets.forEach(function(spreadsheet, i) {
+                    // For Vue performance see VUE PERF NOTE
+                    Object.preventExtensions(jtk_ps[i]);
+                    Object.preventExtensions(jtk_qs[i]);
+                    spreadsheet.jtk_ps = jtk_ps[i];
+                    spreadsheet.jtk_qs = jtk_qs[i];
                 });
             },
             error: function(error) {
@@ -114,7 +109,7 @@
         });
 
         // Load the Upside values
-        if (app.spreadsheets.length > 1) {
+        if (spreadsheets.length > 1) {
             $.ajax({
                 url: "/spreadsheets/get_upside",
                 data: JSON.stringify({'spreadsheet_ids': spreadsheet_ids}),
@@ -131,7 +126,7 @@
                     upside_ps = response['upside_ps'];
                     upside_qs = response['upside_qs'];
 
-                    app.spreadsheets.forEach(function(spreadsheet, idx){
+                    spreadsheets.forEach(function(spreadsheet, idx){
                         Object.preventExtensions(upside_ps[idx]); // See VUE PERF NOTE
                         Object.preventExtensions(upside_qs[idx]); // these aren't covered by above since are one level deeper
                         spreadsheet.upside_ps = upside_ps[idx];
@@ -1310,7 +1305,7 @@ <h5 class="modal-title text-white">SHARE this spreadsheet</h5>
 
                 $.ajax({
                     url: "/spreadsheets/run_pca",
-                    data: JSON.stringify({'spreadsheet_ids': spreadsheet_ids,
+                    data: JSON.stringify({'spreadsheet_ids': app.spreadsheet_ids,
                                           'selected_genes': selected_genes,
                                           'take_logtransform': vm.pca.config.logtransform,
                                           'take_zscore': vm.pca.config.zscore}),
@@ -1674,6 +1669,10 @@ <h5 class="modal-title text-white">SHARE this spreadsheet</h5>
                 // Return all filters, including the 'base' ones and the ones derived from our statistics
                 return filter_data_list_base.concat(stat_filters);
             },
+
+            spreadsheet_ids: function() {
+                return this.spreadsheets.map( function(spreadsheet) {return spreadsheet.spreadsheet_id;});
+            },
         },
 
         watch: {