https://sourceforge.net/p/fcsalyzer/wiki/Usage/Recent changes to UsageenSun, 08 Nov 2020 16:00:59 -0000https://sourceforge.net/p/fcsalyzer/wiki/Usage/<div class="markdown_content"><pre>--- v30 +++ v31 @@ -8,7 +8,6 @@ Open Document | Opens a FCSalyzer document. This command does not open FACS data files. To open a data file, draw a plot into a document. Save Document | Saves the currently selected document under its current name, overwriting the existing file with the same name. However, if the document was not opened from a file, a file dialog will appear to ask for a save name. Save Document As | Saves the currently selected document after showing a file dialog to the user to enter a new name for the document. -Export statistics | Exports all statistics of the current document to a tab-delimited text file. Set Page Format | The Page Format defines the size of a single page of the document and the used page margins. This is also the page size used for printing. Changing the page size causes the document size to change as well, so that all objects (plots etc) still fit onto the document. Objects are not resized, when the page size changes! Set Document Size | A document can consist of multiple pages, arranged in a grid. The maximum grid size is 10 x 10 pages. Print Document | Brings up the printing dialog. FCSalyzer can't save documents as PDF files directly, but you can use a PDF-Printer like PDFCreator to print the documents into PDFs. </pre> </div>Sven MostböckSun, 08 Nov 2020 16:00:59 -0000https://sourceforge.netd3625e896bedadc0d4ed7c68aaf0668c3cb61a9chttps://sourceforge.net/p/fcsalyzer/wiki/Usage/<div class="markdown_content"><pre>--- v29 +++ v30 @@ -32,7 +32,7 @@ --------|--------- Copy | Copies the selected [quadrant](Quadrant), [region](Region), or [marker](Marker) into the internal clipboard. No other object can currently be copied. The information is only stored in the internal clipboard of FCSalyzer and is not available to any other program. This is simply meant as an easy way to use quadrants and markers in many plots. Paste | Pastes the content of the internal clipboard into the currently selected plot(s). Dot plots and density plots accept regions and quadrants, [histogram](Plot) plots accept markers. Existing quadrants will be replaced, existing markers remain. -Duplicate | Duplicates the selected object(s). Plots and [comments](Comment) are duplicated immediately, [annotations](Annotation) and statistics only if they and their respective plots are selected. Quadrants and markers in the plots are also duplicated, but regions shown in the original plot are not shown in the duplicated plot. +Duplicate | Duplicates the selected object(s). [Plots](Plot) and [comments](Comment) are duplicated immediately, [annotations](Annotation) and [statistics](Statistics) only if they and their respective plots are selected. Quadrants and markers in the plots are also duplicated, but regions shown in the original plot are not shown in the duplicated plot. Delete | Deletes the currently selected object(s), which may be plots, comments, statistics, annotations, quadrant, markers, or regions. If a region is deleted, gates using that region are invalidated. ###Plot### @@ -47,10 +47,10 @@ Previous Datafile | Opens the previous data file in the directory of the data file(s) used for the selected plot(s). "Previous" is defined by the order in which the files are presented to FCSalyzer by the operating system; FCSalyzer does not sort the files alphabetically or something like that. Step size ... | Brings up a dialog that allows to change the step size used for "Next" and "Previous Datafile". Step size 1 means the directly next/previous file in the directory, step size 2 means that one file is skipped, etc. Manage color gradients | Brings up a dialog that allows to organize (create, modify, delete) [color gradients](Color Gradients) that are used in density plots. -Annotate | Opens a dialog to select a FCS keyword whose value is then used as an annotation for the selected plot(s). -Statistics | Opens a dialog to select the statistics that are then shown for the selected plot(s). -Edit statistics | Allows to change the the properties of the currently selected statistics. These new properties become the standard for newly created statistics. -Edit markers | Shows a dialog to adjust the markers of the currently selected histogram. If more than one histogram is selected, the first found histogram is changed. +Annotate | Opens a dialog to select a FCS keyword whose value is then used as an [annotation](Annotation) for the selected plot(s). +Statistics | Opens a dialog to select the [statistics](Statistics) that are then shown for the selected plot(s). +Edit statistics | Allows to change the the properties of the currently selected [statistics](Statistics). These new properties become the standard for newly created statistics. +Edit markers | Shows a dialog to adjust the [markers](Marker) of the currently selected histogram. If more than one histogram is selected, the first found histogram is changed. ###Arrangement###  </pre> </div>Sven MostböckSun, 08 Nov 2020 16:00:26 -0000https://sourceforge.netf51b5c936fa3a126832dbe798d3b9c063aa72ba3https://sourceforge.net/p/fcsalyzer/wiki/Usage/<div class="markdown_content"><pre>--- v28 +++ v29 @@ -20,7 +20,7 @@ Command | Effect --------|--------- View File Data | Brings up a [dialog](ViewingData) that lists all currently opened FCS data files with an option to inspect the data of the FCS files. This includes stored metadata such as parameter keywords, and also the event data values. -Format Datafiles | Brings up a dialog that lists all currently opened FCS data files with an option to change [log transformation](Transformation), [compensation](Compensation), [parameter description](Custom Parameter Descriptions) and [parameter multipliers](Multiplying Parameters) of the FCS files. +Format Datafiles | Brings up a dialog that lists all currently opened FCS data files with an option to change [log transformation](Transformation), [compensation](Compensation), [parameter description](Custom parameter descriptions) and [parameter multipliers](Multiplying Parameters) of the FCS files. Derive Parameters | Brings up a dialog that allows the definition of new parameters that are [calculated](Deriving Parameters) based on existing parameters. Attach Parameters | Brings up a dialog that allows to [import and attach data](AttachParameters) as new parameters to FACS data files. Edit Regions / Gates | Shows a dialog to rename [regions](Region) and to create and rename [gates](Gate). </pre> </div>Sven MostböckSun, 08 Nov 2020 15:15:08 -0000https://sourceforge.netbd5e31fe9082322b22b1991c33e5f8409c58ef0bhttps://sourceforge.net/p/fcsalyzer/wiki/Usage/<div class="markdown_content"><pre>--- v27 +++ v28 @@ -40,7 +40,7 @@ Command | Effect --------|--------- -Format Plot/Overlay | Opens the dialog to format the plot and create [overlays](Overlay). +Format Plot/Overlay | Opens the dialog to format the plot and create [overlays](Edit Overlays (Format plot)). Export Plot/Overlay to PNG, data, statistics | Brings up an [export dialog](ExportingData). There are a lot of possibilities: FCSalyzer can export the selected plot(s) as graphic to PNG and SVG. Also, their statistics can be exported to a CSV file, as can be the event data shown in the plots. Especially interesting is the possiblity for batch processing and exporting: a list of FACS data files (FCS files) can be selected and the export cycles through each of the files. Set Datafile | Opens a file dialog to select a new data file for the selected plot(s). Next Datafile | Opens the next data file in the directory of the data file(s) used for the selected plot(s). "Next" is defined by the order in which the files are presented to FCSalyzer by the operating system; FCSalyzer does not sort the files alphabetically or something like that. </pre> </div>Sven MostböckSun, 08 Nov 2020 15:09:21 -0000https://sourceforge.net4c23bb168ecdba4021edb78039daa7751051e09bhttps://sourceforge.net/p/fcsalyzer/wiki/Usage/<div class="markdown_content"><pre>--- v26 +++ v27 @@ -81,6 +81,6 @@ Density Plot | Allows to draw a [density plot](Plot) onto the document. To draw, click and drag the selection border on the document. After releasing the mouse, a file dialog will appear to select the data file for the plot. Histogram | Allows to draw a [histogram plot](Plot) onto the document. To draw, click and drag the selection border on the document. After releasing the mouse, a file dialog will appear to select the data file for the plot. Text Area | Allows to draw a [comment](Comment) onto the document. To draw, click and drag the selection border on the document. After releasing the mouse, an empty text area is created. To enter text, double-click on the area to enter edit mode. The text area's height is adjusted to the content size. -Font size | This combo box allows to change the font size of the currently selected objects. -Percentage | This combo box allows to change the percentages of the shown events in the the currently selected dot plots. -Gate | This combo box allows to change the gates of the currently selected plots. +Font size | This drop-down box allows to change the font size of the currently selected objects. +Percentage | This drop-down box allows to change the percentages of the shown events in the the currently selected dot plots. +Gate | This drop-down box allows to change the gates of the currently selected plots. </pre> </div>Sven MostböckSat, 07 Nov 2020 21:33:29 -0000https://sourceforge.netab2184cee739956ac6bb0a10c519ffc670bcf302https://sourceforge.net/p/fcsalyzer/wiki/Usage/<div class="markdown_content"><pre>--- v25 +++ v26 @@ -1,6 +1,6 @@ ##Menu Bar Items## ###Document### - + Command | Effect --------|--------- @@ -15,7 +15,7 @@ Export Document to PNG, data, statistics | Brings up an [export dialog](ExportingData). There are a lot of possibilities: FCSalyzer can export the whole document as graphic to PNG and SVG. Also, the statistics shown in a document can be exported to a CSV file, as can be the event data shown in the document's plots. Especially interesting is the possiblity for batch processing and exporting: a list of FACS data files (FCS files) can be selected and the export cycles through each of the files. ###Data Files### -![The "Data Files" menu bar](https://sourceforge.net/p/fcsalyzer/wiki/Images/attachment/MenuBar_DataFiles.png "The "Data Files" menu bar") + Command | Effect --------|--------- @@ -26,7 +26,7 @@ Edit Regions / Gates | Shows a dialog to rename [regions](Region) and to create and rename [gates](Gate). ###Edit### -![The "Edit" menu bar](https://sourceforge.net/p/fcsalyzer/wiki/Images/attachment/MenuBar_Edit.png "The "Edit" menu bar") + Command | Effect --------|--------- @@ -36,7 +36,7 @@ Delete | Deletes the currently selected object(s), which may be plots, comments, statistics, annotations, quadrant, markers, or regions. If a region is deleted, gates using that region are invalidated. ###Plot### -![The "Plot" menu bar](https://sourceforge.net/p/fcsalyzer/wiki/Images/attachment/MenuBar_Plot.png "The "Plot" menu bar") + Command | Effect --------|--------- @@ -53,21 +53,22 @@ Edit markers | Shows a dialog to adjust the markers of the currently selected histogram. If more than one histogram is selected, the first found histogram is changed. ###Arrangement### -![The "Arrangement" menu bar](https://sourceforge.net/p/fcsalyzer/wiki/Images/attachment/MenuBar_Arrangement.png "The "Arrangement" menu bar") + Command | Effect --------|------- Move ...| Moves the selected plots by a small increment. Please note that this option is meant for small adjustments of the plot positions. Keeping the arrow keys pressed down does not show smooth movement of the plots, but lets the plots jump around. Align ...| Aligns the selected panels according to the respective out-most panel. So "Align Left" brings all selected panel to the left border to the left-most panel. -###H elp### -![The "Help" menu bar](https://sourceforge.net/p/fcsalyzer/wiki/Images/attachment/MenuBar_Help.png "The "Help" menu bar") +###Help### + Command | Effect --------|--------- About | Shows a small dialog with the GPL3 license under which FCSalyzer is distributed. ###Icon Bar### + The icon bar contains buttons for drawing and adjusting objects in the document. Icon | Effect </pre> </div>Sven MostböckSat, 07 Nov 2020 21:30:25 -0000https://sourceforge.netc9ad0b0032d0b4f2dc54e9db03edb3879bb37a46https://sourceforge.net/p/fcsalyzer/wiki/Usage/<div class="markdown_content"><pre>--- v24 +++ v25 @@ -1,6 +1,6 @@ ##Menu Bar Items## ###Document### -![The "Document" menu bar](https://sourceforge.net/p/fcsalyzer/wiki/Images/attachment/MenuBar_Document.png "The "Document" menu bar") + Command | Effect --------|--------- </pre> </div>Sven MostböckSat, 07 Nov 2020 21:28:29 -0000https://sourceforge.netcb62d4e1e580ea3ff0826d63407ca5522900e962https://sourceforge.net/p/fcsalyzer/wiki/Usage/<div class="markdown_content"><pre>--- v23 +++ v24 @@ -60,7 +60,7 @@ Move ...| Moves the selected plots by a small increment. Please note that this option is meant for small adjustments of the plot positions. Keeping the arrow keys pressed down does not show smooth movement of the plots, but lets the plots jump around. Align ...| Aligns the selected panels according to the respective out-most panel. So "Align Left" brings all selected panel to the left border to the left-most panel. -###Help### +###H elp### ![The "Help" menu bar](https://sourceforge.net/p/fcsalyzer/wiki/Images/attachment/MenuBar_Help.png "The "Help" menu bar") Command | Effect </pre> </div>Sven MostböckSat, 07 Nov 2020 21:27:49 -0000https://sourceforge.net3785e58bba70a23ce5fb8086a6cce73de51bbc45https://sourceforge.net/p/fcsalyzer/wiki/Usage/<div class="markdown_content"><pre>--- v22 +++ v23 @@ -26,7 +26,7 @@ Edit Regions / Gates | Shows a dialog to rename [regions](Region) and to create and rename [gates](Gate). ###Edit### -![The "Edit" menu bar]((https://sourceforge.net/p/fcsalyzer/wiki/Images/attachment/MenuBar_Edit.png "The "Edit" menu bar") +![The "Edit" menu bar](https://sourceforge.net/p/fcsalyzer/wiki/Images/attachment/MenuBar_Edit.png "The "Edit" menu bar") Command | Effect --------|--------- @@ -36,7 +36,7 @@ Delete | Deletes the currently selected object(s), which may be plots, comments, statistics, annotations, quadrant, markers, or regions. If a region is deleted, gates using that region are invalidated. ###Plot### -![The "Plot" menu bar]((https://sourceforge.net/p/fcsalyzer/wiki/Images/attachment/MenuBar_Plot.png "The "Plot" menu bar") +![The "Plot" menu bar](https://sourceforge.net/p/fcsalyzer/wiki/Images/attachment/MenuBar_Plot.png "The "Plot" menu bar") Command | Effect --------|--------- @@ -53,7 +53,7 @@ Edit markers | Shows a dialog to adjust the markers of the currently selected histogram. If more than one histogram is selected, the first found histogram is changed. ###Arrangement### -![The "Arrangement" menu bar]((https://sourceforge.net/p/fcsalyzer/wiki/Images/attachment/MenuBar_Arrangement.png "The "Arrangement" menu bar") +![The "Arrangement" menu bar](https://sourceforge.net/p/fcsalyzer/wiki/Images/attachment/MenuBar_Arrangement.png "The "Arrangement" menu bar") Command | Effect --------|------- @@ -61,7 +61,7 @@ Align ...| Aligns the selected panels according to the respective out-most panel. So "Align Left" brings all selected panel to the left border to the left-most panel. ###Help### -![The "Help" menu bar]((https://sourceforge.net/p/fcsalyzer/wiki/Images/attachment/MenuBar_Help.png "The "Help" menu bar") +![The "Help" menu bar](https://sourceforge.net/p/fcsalyzer/wiki/Images/attachment/MenuBar_Help.png "The "Help" menu bar") Command | Effect --------|--------- </pre> </div>Sven MostböckSat, 07 Nov 2020 21:26:49 -0000https://sourceforge.net67947b985dac9fab5a777ed816c222bde3b19c75https://sourceforge.net/p/fcsalyzer/wiki/Usage/<div class="markdown_content"><pre>--- v21 +++ v22 @@ -1,10 +1,10 @@ ##Menu Bar Items## -###File### -![The "File" menu bar](https://sourceforge.net/p/fcsalyzer/wiki/Usage/attachment/Menu1.jpg "The "File" menu bar") +###Document### +![The "Document" menu bar](https://sourceforge.net/p/fcsalyzer/wiki/Images/attachment/MenuBar_Document.png "The "Document" menu bar") Command | Effect --------|--------- -New Document | Generates a new [document](Document). A document is the canvas onto the [plots](Plot), [statistics](Statistics), etc are drawn. Documents can be saved and printed. +New Document | Generates a new [document](Document). A document is the canvas onto which the [plots](Plot), [statistics](Statistics), etc are drawn. Documents can be saved and printed. Open Document | Opens a FCSalyzer document. This command does not open FACS data files. To open a data file, draw a plot into a document. Save Document | Saves the currently selected document under its current name, overwriting the existing file with the same name. However, if the document was not opened from a file, a file dialog will appear to ask for a save name. Save Document As | Saves the currently selected document after showing a file dialog to the user to enter a new name for the document. @@ -12,20 +12,21 @@ Set Page Format | The Page Format defines the size of a single page of the document and the used page margins. This is also the page size used for printing. Changing the page size causes the document size to change as well, so that all objects (plots etc) still fit onto the document. Objects are not resized, when the page size changes! Set Document Size | A document can consist of multiple pages, arranged in a grid. The maximum grid size is 10 x 10 pages. Print Document | Brings up the printing dialog. FCSalyzer can't save documents as PDF files directly, but you can use a PDF-Printer like PDFCreator to print the documents into PDFs. -Export Document to PNG | Brings up an export dialog. FCSalyzer can export the whole document into PNG files, one PNG file for each page. The export resolution can be selected from 72-900 DPI, leading to differently size PNG image files. +Export Document to PNG, data, statistics | Brings up an [export dialog](ExportingData). There are a lot of possibilities: FCSalyzer can export the whole document as graphic to PNG and SVG. Also, the statistics shown in a document can be exported to a CSV file, as can be the event data shown in the document's plots. Especially interesting is the possiblity for batch processing and exporting: a list of FACS data files (FCS files) can be selected and the export cycles through each of the files. ###Data Files### -![The "Data Files" menu bar](https://sourceforge.net/p/fcsalyzer/wiki/Usage/attachment/Menu2.jpg "The "Data Files" menu bar") +![The "Data Files" menu bar](https://sourceforge.net/p/fcsalyzer/wiki/Images/attachment/MenuBar_DataFiles.png "The "Data Files" menu bar") Command | Effect --------|--------- View File Data | Brings up a [dialog](ViewingData) that lists all currently opened FCS data files with an option to inspect the data of the FCS files. This includes stored metadata such as parameter keywords, and also the event data values. Format Datafiles | Brings up a dialog that lists all currently opened FCS data files with an option to change [log transformation](Transformation), [compensation](Compensation), [parameter description](Custom Parameter Descriptions) and [parameter multipliers](Multiplying Parameters) of the FCS files. Derive Parameters | Brings up a dialog that allows the definition of new parameters that are [calculated](Deriving Parameters) based on existing parameters. +Attach Parameters | Brings up a dialog that allows to [import and attach data](AttachParameters) as new parameters to FACS data files. Edit Regions / Gates | Shows a dialog to rename [regions](Region) and to create and rename [gates](Gate). ###Edit### -![The "Edit" menu bar](https://sourceforge.net/p/fcsalyzer/wiki/Usage/attachment/Menu3.jpg "The "Edit" menu bar") +![The "Edit" menu bar]((https://sourceforge.net/p/fcsalyzer/wiki/Images/attachment/MenuBar_Edit.png "The "Edit" menu bar") Command | Effect --------|--------- @@ -35,16 +36,16 @@ Delete | Deletes the currently selected object(s), which may be plots, comments, statistics, annotations, quadrant, markers, or regions. If a region is deleted, gates using that region are invalidated. ###Plot### -![The "Plot" menu bar](https://sourceforge.net/p/fcsalyzer/wiki/Usage/attachment/Menu4.jpg "The "Plot" menu bar") +![The "Plot" menu bar]((https://sourceforge.net/p/fcsalyzer/wiki/Images/attachment/MenuBar_Plot.png "The "Plot" menu bar") Command | Effect --------|--------- Format Plot/Overlay | Opens the dialog to format the plot and create [overlays](Overlay). -Export Plot/Overlay to PNG | Brings up an export dialog. FCSalyzer can export selected plots into PNG files, one PNG file for each plot. The export resolution can be selected from 72-900 DPI, leading to differently size PNG image files. -Export Plot/Overlay to CSV | Brings up an export dialog. FCSalyzer can export the event data that are shown in selected plots into CSV files, one CSV file for each plot. The event data can be exported as raw data, exactly like stored in the FCS file, or as the [adjusted data](ViewingData) used for statistics calculations. +Export Plot/Overlay to PNG, data, statistics | Brings up an [export dialog](ExportingData). There are a lot of possibilities: FCSalyzer can export the selected plot(s) as graphic to PNG and SVG. Also, their statistics can be exported to a CSV file, as can be the event data shown in the plots. Especially interesting is the possiblity for batch processing and exporting: a list of FACS data files (FCS files) can be selected and the export cycles through each of the files. Set Datafile | Opens a file dialog to select a new data file for the selected plot(s). Next Datafile | Opens the next data file in the directory of the data file(s) used for the selected plot(s). "Next" is defined by the order in which the files are presented to FCSalyzer by the operating system; FCSalyzer does not sort the files alphabetically or something like that. Previous Datafile | Opens the previous data file in the directory of the data file(s) used for the selected plot(s). "Previous" is defined by the order in which the files are presented to FCSalyzer by the operating system; FCSalyzer does not sort the files alphabetically or something like that. +Step size ... | Brings up a dialog that allows to change the step size used for "Next" and "Previous Datafile". Step size 1 means the directly next/previous file in the directory, step size 2 means that one file is skipped, etc. Manage color gradients | Brings up a dialog that allows to organize (create, modify, delete) [color gradients](Color Gradients) that are used in density plots. Annotate | Opens a dialog to select a FCS keyword whose value is then used as an annotation for the selected plot(s). Statistics | Opens a dialog to select the statistics that are then shown for the selected plot(s). @@ -52,15 +53,15 @@ Edit markers | Shows a dialog to adjust the markers of the currently selected histogram. If more than one histogram is selected, the first found histogram is changed. ###Arrangement### -![The "Arrangement" menu bar](https://sourceforge.net/p/fcsalyzer/wiki/Usage/attachment/Menu5.jpg "The "Arrangement" menu bar") +![The "Arrangement" menu bar]((https://sourceforge.net/p/fcsalyzer/wiki/Images/attachment/MenuBar_Arrangement.png "The "Arrangement" menu bar") Command | Effect --------|------- Move ...| Moves the selected plots by a small increment. Please note that this option is meant for small adjustments of the plot positions. Keeping the arrow keys pressed down does not show smooth movement of the plots, but lets the plots jump around. Align ...| Aligns the selected panels according to the respective out-most panel. So "Align Left" brings all selected panel to the left border to the left-most panel. -###H elp### -![The "Help" menu bar](https://sourceforge.net/p/fcsalyzer/wiki/Usage/attachment/Menu6.jpg "The "Help" menu bar") +###Help### +![The "Help" menu bar]((https://sourceforge.net/p/fcsalyzer/wiki/Images/attachment/MenuBar_Help.png "The "Help" menu bar") Command | Effect --------|--------- </pre> </div>Sven MostböckSat, 07 Nov 2020 21:25:12 -0000https://sourceforge.net0bc94134d2f6ffc28c56b36e413d8ad88bc43270