Recent changes to Examples

Examples modified by Vincent Delorme

Vincent Delorme — Mon, 29 May 2023 04:09:19 -0000

--- v12
+++ v13
@@ -145,8 +145,27 @@
 - Loading a layout file and playing around with the layout and Sample-type areas.
 - Defining combination layouts using multiple layers.
 - Attaching a single-plate result file, parsing and mapping, validation and heatmap visualization.
-- Using the "Column Analysis" tool to see data aggregation for combinatons.
+- Using the "Column Analysis" tool to see data aggregation for combinations.

 **How to:**
 When importing the result file, all parsing options can be left to their default values. Map the "Data" column for import.
 Open the "Column Analysis" tool to see the data aggregation accross all the computed combinations.
+
+Grouping example
+----------------
+
+Download the files here: [Grouping.zip](https://plateeditor.sourceforge.io/examples/Grouping.zip)
+**Archive contents:**
+- Layout_Groups.save: layout file for this example that can be loaded in _PlateEditor_.
+- Definition_Groups.txt: text file containing the definition for 2 plates, for the range "Range" defined in the layout. The definition should be mapped to the "Definition" column, only column present in the file.
+- Results_Groups.xlsx: excel file containing the data for this plate. The file can be mapped with a Well ID ("Well"). The "Data" column should be imported as a numeric type.
+
+**Available with this example:**
+- Loading a layout file and playing around with the layout and Range-type areas.
+- Defining combination layouts using multiple layers.
+- Attaching a single-plate result file, parsing and mapping, validation and heatmap visualization.
+- Using the "Grouped Analysis" tool to see data aggregation for combinations.
+
+**How to:**
+When importing the result file, all parsing options can be left to their default values. Map the "Data" column for import.
+Open the "Grouped Analysis" tool to see the how the data aggregates when setting up different combinations and levels of aggregation.

Examples modified by Vincent Delorme

Vincent Delorme — Sat, 27 Nov 2021 12:11:30 -0000

--- v11
+++ v12
@@ -35,12 +35,13 @@
 - Min & Max options for multiple plates.
 - Pairing result and definition plates using the auto-pairing functions.
 - Using the "Controls" tool to see the calculation of controls for multiple plates
+- Using the "Hits" tool to select values above a given threshold

 **How to:**
 When importing the definition file, all parsing options can be left to their default values. Map the "CPD ID" column to the Definition role.
 When importing the result file, all parsing options can be left to their default values. Map the "RFU" column for import.
 Pair the result and definition plates using the auto-pairing function (By plate name). There should be 162 matches.
-Change the Min & Max option to "Plate" and browse the result plates to identify hits.
+Change the Min & Max option to "Plate" and browse the result plates to identify hits. This can be done automatically with the "Hits" tool, after selecting the desired threshold.
 Open the "Controls" tool and run the "Compute All" function to start the plate analysis process (see below).
 [[img src="Example_Screening.jpg" alt="Screening example - Compute all"]]

@@ -60,12 +61,13 @@
 - Min & Max options for multiple plates.
 - Pairing result and definition plates using the auto-pairing functions.
 - Using the "Controls" tool to see the calculation of controls for multiple plates
+- Using the "Hits" tool to select values above a given threshold

 **How to:**
 When importing the definition file, all parsing options can be left to their default values. Map the "Cpd ID" column to the Definition role.
 When importing the result file, all parsing options can be left to their default values. Map the "RFU" column for import.
 Pair the result and definition plates using the auto-pairing function (By plate name). There should be 10 matches.
-Browse the result plates to identify hits.
+Browse the result plates to identify hits. This can be done automatically with the "Hits" tool, after selecting the desired threshold.
 Open the "Controls" tool and run the "Compute All" function to start the plate analysis process (see example above).

 DRC example

Examples modified by Vincent Delorme

Vincent Delorme — Thu, 29 Apr 2021 00:10:53 -0000

--- v10
+++ v11
@@ -85,3 +85,66 @@
 When importing the result file, all parsing options can be left to their default values. Map the "Data" column for import.
 Open the "Grouped Analysis" tool and select the concentration as rows, the Range as columns (see below).
 [[img src="Example_DRC.jpg" alt="DRC example - Grouped analysis"]]
+
+DRC2 example
+----------------
+
+Download the files here: [DRC2.zip](https://plateeditor.sourceforge.io/examples/DRC2.zip)
+**Archive contents:**
+- Layout.save: layout file for this example that can be loaded in _PlateEditor_.
+- Definition.txt: text file containing the definition for the range "compounds" defined in the layout.
+- Results.xlsx: excel file containing the data for this plate. The file can be mapped with a Well ID ("Well"). The "Data" column should be imported as a numeric type.
+
+**Available with this example:**
+- Loading a layout file and playing around with the layout and Range-type areas.
+- Attaching a single-plate definition file, parsing and mapping, plate visualization with Plate view.
+- Attaching a single-plate result file, parsing and mapping, validation and heatmap visualization.
+- Using the "Grouped Analysis" tool to see grouped aggregation for dose-response.
+
+**How to:**
+When importing the definition file, all parsing options can be left to their default values. Map the "Name" column to the Definition role.
+When importing the result file, all parsing options can be left to their default values. Map the "Data" column for import.
+Open the "Grouped Analysis" tool and select the concentration as rows, the Range as columns (see example above).
+Note the automatic resolution of names for each range items
+
+DRC3 example
+----------------
+
+Download the files here: [DRC3.zip](https://plateeditor.sourceforge.io/examples/DRC3.zip)
+**Archive contents:**
+- Layout.save: layout file for this example that can be loaded in _PlateEditor_.
+- Definition.txt: text file containing the definition for the range "compounds" defined in the layout.
+- Results.xlsx: excel file containing the data for all plates. The file can be mapped with a Well ID ("Well") and a Plate ID ("Plate"). The "Data" column should be imported as a numeric type.
+
+**Available with this example:**
+- Loading a layout file and playing around with the layout and Range-type areas.
+- Attaching a multi-plate definition file, parsing and mapping, plate visualization with Plate view.
+- Attaching a multi-plate result file, parsing and mapping, validation and heatmap visualization.
+- Min & Max options for multiple plates.
+- Pairing result and definition plates using the auto-pairing functions.
+- Using the "Grouped Analysis" tool to see grouped aggregation for dose-response, in a multi-plate setup.
+
+**How to:**
+When importing the definition file, all parsing options can be left to their default values. Map the "Name" column to the Definition role.
+When importing the result file, all parsing options can be left to their default values. Map the "Data" column for import.
+Pair the result and definition plates using the auto-pairing function (By plate index). There should be 3 matches.
+Open the "Grouped Analysis" tool and select the concentration as rows, the Range as columns (see example above).
+Browse the result plates. Note the automatic resolution of names for each range items, at the plate level.
+
+Infection example
+----------------
+
+Download the files here: [Infection.zip](https://plateeditor.sourceforge.io/examples/Infection.zip)
+**Archive contents:**
+- Layout.save: layout file for this example that can be loaded in _PlateEditor_.
+- Results.xlsx: excel file containing the data for this plate. The file can be mapped with a Well ID ("Well"). The "Data" column should be imported as a numeric type.
+
+**Available with this example:**
+- Loading a layout file and playing around with the layout and Sample-type areas.
+- Defining combination layouts using multiple layers.
+- Attaching a single-plate result file, parsing and mapping, validation and heatmap visualization.
+- Using the "Column Analysis" tool to see data aggregation for combinatons.
+
+**How to:**
+When importing the result file, all parsing options can be left to their default values. Map the "Data" column for import.
+Open the "Column Analysis" tool to see the data aggregation accross all the computed combinations.

Examples modified by Vincent Delorme

Vincent Delorme — Wed, 28 Apr 2021 23:56:18 -0000

--- v9
+++ v10
@@ -1,22 +1,21 @@
 # Examples

 A bit lost with _PlateEditor_? To get you started, you can follow the proposed examples, using the files available in the bundled application or dowloadable throughout this tutorial.
-To download the files without leaving this page, do a left-click on its name and choose "". Save the files locally in your hard-disk to import them later in PlateEditor.

 Simple example
 ----------------

 Download the files here: [Simple.zip](https://plateeditor.sourceforge.io/examples/Simple.zip)
-Archive contents:
+**Archive contents:**
 - Layout.save: layout file for this example that can be loaded in _PlateEditor_.
 - Results_example1.txt: text file containing the data for this plate. The file can be mapped with a Well ID ("Well"). The "Cell count" column should be imported as a numeric type.

-Available with this example:
+**Available with this example:**
 - Loading a layout file and playing around with the layout and Sample-type areas.
 - Attaching a single-plate result file, parsing and mapping, validation and heatmap visualization.
 - Using the "Column Analysis" feature to see data aggregation.

-How to:
+**How to:**
 When importing the result file, all parsing options can be left to their default values. Map the "Cell count" column for import, as in the picture below.
 [[img src="Example_Simple.jpg" alt="Simple example - Mapping for the result file"]]

@@ -24,12 +23,12 @@
 ----------------

 Download the files here: [Screening.zip](https://plateeditor.sourceforge.io/examples/Screening.zip)
-Archive contents:
+**Archive contents:**
 - Layout.save: layout file for this example that can be loaded in _PlateEditor_.
 - Definition.csv: csv file containing the definition for the range "cpds" defined in the layout.
 - Results.xlsx: excel file containing the results for all plates. The file can be mapped with a Well ID ("Well") and a Plate ID ("Plate ID"). The "RFU" column should be imported as a numeric type.

-Available with this example:
+**Available with this example:**
 - Loading a layout file and playing around with the layout and Control-type, Range-type areas.
 - Attaching a multi-plate definition file, parsing and mapping, plate visualization with Plate view.
 - Attaching a multi-plate result file, parsing and mapping, validation and heatmap visualization, plate browsing.
@@ -37,10 +36,52 @@
 - Pairing result and definition plates using the auto-pairing functions.
 - Using the "Controls" tool to see the calculation of controls for multiple plates

-How to:
+**How to:**
 When importing the definition file, all parsing options can be left to their default values. Map the "CPD ID" column to the Definition role.
 When importing the result file, all parsing options can be left to their default values. Map the "RFU" column for import.
 Pair the result and definition plates using the auto-pairing function (By plate name). There should be 162 matches.
 Change the Min & Max option to "Plate" and browse the result plates to identify hits.
 Open the "Controls" tool and run the "Compute All" function to start the plate analysis process (see below).
 [[img src="Example_Screening.jpg" alt="Screening example - Compute all"]]
+
+Screening2 example
+----------------
+
+Download the files here: [Screening2.zip](https://plateeditor.sourceforge.io/examples/Screening2.zip)
+**Archive contents:**
+- Layout.save: layout file for this example that can be loaded in _PlateEditor_.
+- Definition.txt: text file containing the definition for the range "compounds" defined in the layout.
+- Results.txt: text file containing the results for all plates. The file can be mapped with a Well ID ("Well") and a Plate ID ("Plate ID"). The "RFU" column should be imported as a numeric type.
+
+**Available with this example:**
+- Loading a layout file and playing around with the layout and Control-type, Range-type areas.
+- Attaching a multi-plate definition file, parsing and mapping, plate visualization with Plate view.
+- Attaching a multi-plate result file, parsing and mapping, validation and heatmap visualization, plate browsing.
+- Min & Max options for multiple plates.
+- Pairing result and definition plates using the auto-pairing functions.
+- Using the "Controls" tool to see the calculation of controls for multiple plates
+
+**How to:**
+When importing the definition file, all parsing options can be left to their default values. Map the "Cpd ID" column to the Definition role.
+When importing the result file, all parsing options can be left to their default values. Map the "RFU" column for import.
+Pair the result and definition plates using the auto-pairing function (By plate name). There should be 10 matches.
+Browse the result plates to identify hits.
+Open the "Controls" tool and run the "Compute All" function to start the plate analysis process (see example above).
+
+DRC example
+----------------
+
+Download the files here: [DRC.zip](https://plateeditor.sourceforge.io/examples/DRC.zip)
+**Archive contents:**
+- Layout.save: layout file for this example that can be loaded in _PlateEditor_.
+- Results.csv: csv file containing the data for this plate. The file can be mapped with a Well ID ("Well"). The "Data" column should be imported as a numeric type.
+
+**Available with this example:**
+- Loading a layout file and playing around with the layout and Range-type areas.
+- Attaching a single-plate result file, parsing and mapping, validation and heatmap visualization.
+- Using the "Grouped Analysis" tool to see grouped aggregation for dose-response.
+
+**How to:**
+When importing the result file, all parsing options can be left to their default values. Map the "Data" column for import.
+Open the "Grouped Analysis" tool and select the concentration as rows, the Range as columns (see below).
+[[img src="Example_DRC.jpg" alt="DRC example - Grouped analysis"]]

Examples modified by Vincent Delorme

Vincent Delorme — Wed, 28 Apr 2021 23:39:09 -0000

--- v8
+++ v9
@@ -8,14 +8,39 @@

 Download the files here: [Simple.zip](https://plateeditor.sourceforge.io/examples/Simple.zip)
 Archive contents:
-- Layout.save: layout file for this example that can be loaded in PlateEditor.
+- Layout.save: layout file for this example that can be loaded in _PlateEditor_.
 - Results_example1.txt: text file containing the data for this plate. The file can be mapped with a Well ID ("Well"). The "Cell count" column should be imported as a numeric type.

 Available with this example:
-- Loading a layout file and playing around with the layout and areas.
-- Attaching a result file, parsing and mapping, validation and heatmap visualization.
+- Loading a layout file and playing around with the layout and Sample-type areas.
+- Attaching a single-plate result file, parsing and mapping, validation and heatmap visualization.
 - Using the "Column Analysis" feature to see data aggregation.

 How to:
 When importing the result file, all parsing options can be left to their default values. Map the "Cell count" column for import, as in the picture below.
 [[img src="Example_Simple.jpg" alt="Simple example - Mapping for the result file"]]
+
+Screening example
+----------------
+
+Download the files here: [Screening.zip](https://plateeditor.sourceforge.io/examples/Screening.zip)
+Archive contents:
+- Layout.save: layout file for this example that can be loaded in _PlateEditor_.
+- Definition.csv: csv file containing the definition for the range "cpds" defined in the layout.
+- Results.xlsx: excel file containing the results for all plates. The file can be mapped with a Well ID ("Well") and a Plate ID ("Plate ID"). The "RFU" column should be imported as a numeric type.
+
+Available with this example:
+- Loading a layout file and playing around with the layout and Control-type, Range-type areas.
+- Attaching a multi-plate definition file, parsing and mapping, plate visualization with Plate view.
+- Attaching a multi-plate result file, parsing and mapping, validation and heatmap visualization, plate browsing.
+- Min & Max options for multiple plates.
+- Pairing result and definition plates using the auto-pairing functions.
+- Using the "Controls" tool to see the calculation of controls for multiple plates
+
+How to:
+When importing the definition file, all parsing options can be left to their default values. Map the "CPD ID" column to the Definition role.
+When importing the result file, all parsing options can be left to their default values. Map the "RFU" column for import.
+Pair the result and definition plates using the auto-pairing function (By plate name). There should be 162 matches.
+Change the Min & Max option to "Plate" and browse the result plates to identify hits.
+Open the "Controls" tool and run the "Compute All" function to start the plate analysis process (see below).
+[[img src="Example_Screening.jpg" alt="Screening example - Compute all"]]

Examples modified by Vincent Delorme

Vincent Delorme — Wed, 28 Apr 2021 23:18:26 -0000

--- v7
+++ v8
@@ -1,14 +1,21 @@
 # Examples

-A bit lost with _PlateEditor_? To get you started, you can follow the proposed examples, using the files available in the bundled application or downloadable throughout this tutorial. Save the files locally in your hard-disk to import them later in _PlateEditor_.
+A bit lost with _PlateEditor_? To get you started, you can follow the proposed examples, using the files available in the bundled application or dowloadable throughout this tutorial.
+To download the files without leaving this page, do a left-click on its name and choose "". Save the files locally in your hard-disk to import them later in PlateEditor.

 Simple example
 ----------------

-Related files:
-- [Layout.save](https://plateeditor.sourceforge.io/examples/Simple/Layout.save): layout file for this example that can be loaded in _PlateEditor_.
--[Results_example1.txt](https://plateeditor.sourceforge.io/examples/Simple/Results_example1.txt): text file containing the data for this plate. The file can be mapped with a Well ID ("Well"). The "Cell count" column should be imported as a numeric type.
+Download the files here: [Simple.zip](https://plateeditor.sourceforge.io/examples/Simple.zip)
+Archive contents:
+- Layout.save: layout file for this example that can be loaded in PlateEditor.
+- Results_example1.txt: text file containing the data for this plate. The file can be mapped with a Well ID ("Well"). The "Cell count" column should be imported as a numeric type.

-How-to:
-Load the layout file and play around with the layout and areas. Attach the result file, map the "Cell count" column to import as in the picture below and play around with the resulting heatmap. You can use the "Column Analysis" feature with this example to see how data aggregation looks like.
+Available with this example:
+- Loading a layout file and playing around with the layout and areas.
+- Attaching a result file, parsing and mapping, validation and heatmap visualization.
+- Using the "Column Analysis" feature to see data aggregation.
+
+How to:
+When importing the result file, all parsing options can be left to their default values. Map the "Cell count" column for import, as in the picture below.
 [[img src="Example_Simple.jpg" alt="Simple example - Mapping for the result file"]]

Examples modified by Vincent Delorme

Vincent Delorme — Wed, 28 Apr 2021 08:35:08 -0000

--- v6
+++ v7
@@ -6,7 +6,6 @@
 ----------------

 Related files:
-Layout.save
 - [Layout.save](https://plateeditor.sourceforge.io/examples/Simple/Layout.save): layout file for this example that can be loaded in _PlateEditor_.
 -[Results_example1.txt](https://plateeditor.sourceforge.io/examples/Simple/Results_example1.txt): text file containing the data for this plate. The file can be mapped with a Well ID ("Well"). The "Cell count" column should be imported as a numeric type.

Examples modified by Vincent Delorme

Vincent Delorme — Wed, 28 Apr 2021 08:33:06 -0000

--- v5
+++ v6
@@ -1,13 +1,13 @@
 # Examples

-A bit lost with _PlateEditor_? To get you started, you can follow the proposed examples, using the files available in the bundled application or dowloadable throughout this tutorial.
-To download the files without leaving this page, do a left-click on its name and choose "". Save the files locally in your hard-disk to import them later in PlateEditor.
+A bit lost with _PlateEditor_? To get you started, you can follow the proposed examples, using the files available in the bundled application or downloadable throughout this tutorial. Save the files locally in your hard-disk to import them later in _PlateEditor_.

 Simple example
 ----------------

 Related files:
-- [Layout.save](https://plateeditor.sourceforge.io/examples/Simple/Layout.save): layout file for this example that can be loaded in PlateEditor.
+Layout.save
+- [Layout.save](https://plateeditor.sourceforge.io/examples/Simple/Layout.save): layout file for this example that can be loaded in _PlateEditor_.
 -[Results_example1.txt](https://plateeditor.sourceforge.io/examples/Simple/Results_example1.txt): text file containing the data for this plate. The file can be mapped with a Well ID ("Well"). The "Cell count" column should be imported as a numeric type.

 How-to:

Examples modified by Vincent Delorme

Vincent Delorme — Wed, 28 Apr 2021 07:51:37 -0000

--- v4
+++ v5
@@ -7,8 +7,8 @@
 ----------------

 Related files:
-- [Layout.save]: layout file for this example that can be loaded in PlateEditor.
-- [Results_example1.txt]: text file containing the data for this plate. The file can be mapped with a Well ID ("Well"). The "Cell count" column should be imported as a numeric type.
+- [Layout.save](https://plateeditor.sourceforge.io/examples/Simple/Layout.save): layout file for this example that can be loaded in PlateEditor.
+-[Results_example1.txt](https://plateeditor.sourceforge.io/examples/Simple/Results_example1.txt): text file containing the data for this plate. The file can be mapped with a Well ID ("Well"). The "Cell count" column should be imported as a numeric type.

 How-to:
 Load the layout file and play around with the layout and areas. Attach the result file, map the "Cell count" column to import as in the picture below and play around with the resulting heatmap. You can use the "Column Analysis" feature with this example to see how data aggregation looks like.

Examples modified by Vincent Delorme

Vincent Delorme — Wed, 28 Apr 2021 07:50:00 -0000

--- v3
+++ v4
@@ -7,8 +7,8 @@
 ----------------

 Related files:
-- [Layout.save](https://plateeditor.sourceforge.io/examples/Simple/Layout.save): layout file for this example that can be loaded in PlateEditor.
-- [Results_example1.txt](https://plateeditor.sourceforge.io/examples/Simple/Results_example1.txt): text file containing the data for this plate. The file can be mapped with a Well ID ("Well"). The "Cell count" column should be imported as a numeric type.
+- [Layout.save]: layout file for this example that can be loaded in PlateEditor.
+- [Results_example1.txt]: text file containing the data for this plate. The file can be mapped with a Well ID ("Well"). The "Cell count" column should be imported as a numeric type.

 How-to:
 Load the layout file and play around with the layout and areas. Attach the result file, map the "Cell count" column to import as in the picture below and play around with the resulting heatmap. You can use the "Column Analysis" feature with this example to see how data aggregation looks like.