ChronQC 1.0.2 version changes

nilesh-tawari · Aug 3, 2017 · 381bb6d · 381bb6d
1 parent b363c2c
commit 381bb6d
Show file tree

Hide file tree

Showing 8 changed files with 62 additions and 33 deletions.
diff --git a/HISTORY.rst b/HISTORY.rst
@@ -2,17 +2,5 @@
 
 History
 -------
-1.0.2: Changes
-
-* Added stacked bar plot and bar and line plot
-* Bug fixes
-* Error handling
-
-1.0.1: Features
-
-* Designed for quality control based on historical data
-* Generates interactive time-series plots for various metrics, allowing comparison of the current run to historical runs
-* Record users' notes and corrective actions directly onto the graphs for long-term record-keeping
-* Provides highly customizable different chart types
-* Supports customized database for plotting
-* Works with output of MultiQC
+July 13, 2017 - Released version 1.0.1 software package
+July 13, 2017 - Released version 1.0.0 software package 
diff --git a/chronqc/chronqc_plot.py b/chronqc/chronqc_plot.py
@@ -275,7 +275,7 @@ def absolute_threshold(df, column, lower_threshold=np.nan, upper_threshold=np.na
     return df_bq
 
 
-def box_whisker_plot(df, ColumnName, Type=''):
+def box_whisker_plot(df, ColumnName, Type='', lower_threshold=np.nan, upper_threshold=np.nan):
     """
     (df) -> df
     generate box plot data form the df
@@ -337,10 +337,13 @@ def box_whisker_plot(df, ColumnName, Type=''):
                                          'Run', 'Sample'])
     df_bp['Sample'].fillna('NA', inplace=True)
     df_bp['Run'].fillna('NA', inplace=True)
+    # set threshold
+    df_bp['lower_threshold'] = float(lower_threshold)
+    df_bp['upper_threshold'] = float(upper_threshold)
     # Add dumy dates at begnining and end of dataframe
     df_bp = add_dates(df_bp)
     # Format data for writing to html file
-    df_bp['Data'] = df_bp[['Date', '25%', '75%', 'Upper_whisker', 'Lower_whisker', '50%', 'Outlier']].values.tolist()
+    df_bp['Data'] = df_bp[['Date', '25%', '75%', 'Upper_whisker', 'Lower_whisker', '50%', 'Outlier', 'upper_threshold', 'lower_threshold']].values.tolist()
     df_bp = format_date_names(df_bp)
     return df_bp
 
@@ -682,14 +685,18 @@ def main(args):
             chart_title = chart["chart_properties"].get('chart_title', t)
             y_label = chart["chart_properties"].get('y_label', y)
             Type = chart["chart_properties"].get("Type", '')
+            lower_threshold = chart["chart_properties"].get("lower_threshold", np.nan) 
+            upper_threshold = chart["chart_properties"].get("upper_threshold", np.nan)
             js_tmpl = string.Template(open(op.join(templates_dir, "box_whisker_plot.txt")).read())
             if not column_name in df.columns:
                 logger.critical("FATAL: no {0} column found in {1}".format(column_name, table))
                 sys.exit(1)
             if Type != '':
-                df_chart = box_whisker_plot(df, column_name, Type=Type)
+                df_chart = box_whisker_plot(df, column_name, Type=Type, 
+                                        lower_threshold=lower_threshold,
+                                        upper_threshold=upper_threshold)
             else:
-                df_chart = box_whisker_plot(df, column_name)
+                df_chart = box_whisker_plot(df, column_name, lower_threshold=lower_threshold, upper_threshold=upper_threshold)
             logger.info("For {0}: {1} data points will be written to html".format(chart_id, len(df_chart)))
         elif chart['chart_type'] == 'time_series_with_bar_line_plot':
             if categories == '':

diff --git a/chronqc/templates/base_template.html b/chronqc/templates/base_template.html
@@ -771,7 +771,7 @@
         function candlePlotter(e) {
 
 		if (e.seriesIndex !== 0) return;
-		var BAR_WIDTH = 12;
+		var BAR_WIDTH = 18;
         var prices = [];
         var price;
         var sets = e.allSeriesPoints;

diff --git a/chronqc/templates/box_whisker_plot.txt b/chronqc/templates/box_whisker_plot.txt
@@ -19,7 +19,7 @@
     	document.getElementById("$divname"),
 		$dataname, 
 		{
-            labels: ["Date","1st Quantile","3rd Quantile","Upper Whisker", "Lower Whisker", "Median","Scatter"],
+            labels: ["Date","1st Quantile","3rd Quantile","Upper Whisker", "Lower Whisker", "Median","Scatter", "Upper Threshold", "Lower Threshold"],
 			labelsDiv: document.getElementById("$labeldiv"),
 			labelsSeparateLines: true,
 			showRangeSelector: true,
@@ -59,8 +59,18 @@
 								+ "<br><b>Median:</b> ".fontcolor("#7e04a3") + data[5] 
 								+ "<br><b>1st Quantile:</b> ".fontcolor("#4DD8AD") + data[1] 
 								+ "<br><b>Lower Whisker:</b> ".fontcolor("#f442d1") + data[4] 
-								+ "<br><b>Outlier:</b> ".fontcolor("#0080ff") + data[6] 
-
+
+						if (data[6] != null){
+							text = text + "<br><b>Outlier:</b> ".fontcolor("#0080ff") + data[6] 
+						}
+
+						if (data[7] != null){
+							text = text + "<br><b>Upper Threshold:</b> ".fontcolor("#ff0000") + data[7] 
+						}
+
+						if (data[8] != null){
+							text = text + "<br><b>Lower Threshold:</b> ".fontcolor("#ff0000") + data[8] 
+						}
 
 						if (run[1].length == 0){return text}
 						else if (run[1].length != 0){
@@ -95,6 +105,18 @@
 					color: "#0080ff",
 					plotter: Dygraph.Plotters.linePlotter,
 					strokeWidth: 0
+				},
+				"Upper Threshold" : {
+					plotter: Dygraph.Plotters.linePlotter,
+					strokePattern: Dygraph.DASHED_LINE ,
+					color: "#ff0000",
+					strokeWidth: 2, 
+				},
+				"Lower Threshold" : {
+					plotter: Dygraph.Plotters.linePlotter,
+					strokePattern: Dygraph.DASHED_LINE ,
+					color: "#ff0000",
+					strokeWidth: 2, 
 				}
 			},	
 			underlayCallback: function(canvas, area, g) {		
@@ -135,11 +157,14 @@
 
 			},
 			pointClickCallback: function(e, point) {
-				run = $runname[point.idx][0]
-				date = $dataname[point.idx][0]
-				date =  moment(date).format("DD-MM-YYYY")
-				//copyToClipboard(run)
-				makeQuery(run,date)
+				if($dataname[point.idx][6] == null)return;
+				else{
+					run = $runname[point.idx][0]
+					date = $dataname[point.idx][0]
+					date =  moment(date).format("DD-MM-YYYY")
+					//copyToClipboard(run)
+					makeQuery(run,date)
+				}
 			},
 		}
 	);		

diff --git a/docs/plots/time_series_with_stacked_bar_plot.rst b/docs/plots/time_series_with_stacked_bar_plot.rst
@@ -52,7 +52,7 @@ Example JSON entry (full) to plot all samples excluding NTC ::
        "table_name": "VCS_Stats_Summary",
        "include_samples": "all",
        "exclude_samples": "NTC",
-       "chart_type": "time_series_with_bar_line_plot",
+       "chart_type": "time_series_with_stacked_bar_plot",
        "chart_properties": {
             "chart_title": "Monthly bar and line plot for Gene (KRAS, KIT, BRAF, PDGFRA, NRAS)",
             "y_value": "Gene",

diff --git a/docs/plots/timeseries_absolute_threshold.rst b/docs/plots/timeseries_absolute_threshold.rst
@@ -35,10 +35,10 @@ Chart Properties
 |                  |                                   | E.g. 100.                                                                                     |
 +------------------+-----------------------------------+-----------------------------------------------------------------------------------------------+
 | upper_threshold  | Integer (Optional)                | This is used to create upper threshold line on the chart.                                     |
-|                  |                                   | E.g.300.                                                                                      |
+|                  |                                   | E.g. 300.                                                                                     |
 +------------------+-----------------------------------+-----------------------------------------------------------------------------------------------+
-| per_sample       | Boolean (Optional)                | Plot per sample graph. Default is “False”.                                                    |
-|                  |                                   | If set to “True” per sample graph will be plotted.                                            |
+| per_sample       | Boolean (Optional)                | Plot per sample graph. Default is "False".                                                    |
+|                  |                                   | If set to "True" per sample graph will be plotted.                                            |
 +------------------+-----------------------------------+-----------------------------------------------------------------------------------------------+
 
 

diff --git a/docs/plots/timeseries_box_whisker.rst b/docs/plots/timeseries_box_whisker.rst
@@ -31,7 +31,12 @@ Chart Properties
 | Type             | String (Optional)                 | This is used to select subset of rows from the SQLite table's "Type" columns.                 |
 |                  |                                   | E.g. "SNPs".                                                                                  |
 +------------------+-----------------------------------+-----------------------------------------------------------------------------------------------+
-
+| lower_threshold  | Integer (Optional)                | This is used to create lower threshold line on the chart.                                     |
+|                  |                                   | E.g. 100.                                                                                     |
++------------------+-----------------------------------+-----------------------------------------------------------------------------------------------+
+| upper_threshold  | Integer (Optional)                | This is used to create upper threshold line on the chart.                                     |
+|                  |                                   | E.g. 300.                                                                                      |
++------------------+-----------------------------------+-----------------------------------------------------------------------------------------------+
 
 Example JSON entry (minimum)::
 
@@ -56,7 +61,9 @@ Example JSON entry (full) to plot all samples excluding HCT15 and NTC ::
            "chart_title": "Bcftools Stats Number Of Snps Monthly Box-and-Whisker Plot",
            "y_value": "Number",
            "Type": "SNPs",
-           "y_label": "Bcftools Stats Number Of Snps"
+           "y_label": "Bcftools Stats Number Of Snps",
+           "lower_threshold": 10000,
+           "upper_threshold": 15000
            }
       }
      ]

diff --git a/examples/custom_db_example/config.json b/examples/custom_db_example/config.json
@@ -136,6 +136,8 @@
       "chart_title": "Number of indels found in Samples Over Time",
       "y_value": "Number",
       "Type": "Indels",
+      "lower_threshold": 1521,
+      "upper_threshold": 1960,
       "y_label": "Number of indels found in each sample"
     }
   },