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| Most operations in FlowJo are point-and-click oriented rather than menu-based. Thus, there are relatively few menu items specific to FlowJo. Click on each menu item to go directly to that information (all information is contained on this page).
Some menu items change when you hold down the option key. You can select a menu, and press or release the option key to see the changes in the menu items. In general, a menu item which changes when the option key is depressed changes the functionality of that menu item to apply to many cases (for example, when a graph window is front-most, close will remove only that window, whereas option-close will remove all graph windows). Where option key menus are different, both are shown (the lower will be with the option key depressed). Apple Menu About FlowJo Contains information about the current version of the program. Help... Launches a web browser with the main help pages. File Menu New Opens a new, empty workspace. Open Workspace... Open an existing workspace. Use the Macintosh standard file open dialog to select a workspace that you have previously created. Close Close the current window. If you close the workspace, FlowJo will confirm whether or not to save any changes you have made. If you hold down the option key and a graph window is front-most, then FlowJo will close all open graph windows. Save Save the current workspace. If it has never been saved before, FlowJo will prompt you for a filename and directory location. Save as... Save the current workspace as a different file. Save as Template Saves a version of the current workspace with all of the samples removed, so that it is easy to construct new analyses simply by adding new samples to the template. Revert Discard all of the changes you have made to this workspace and revert to the last-saved version of the workspace. Page Setup... Define the characteristics about any printing you will do from FlowJo. Print... Print the current window. See the page on Printing. Quit Quit FlowJo. If necessary, FlowJo will ask you to save any changes to open workspaces.
Edit Menu Undo Currently disabled for all but text editing functions. Cut When editing text fields, or working in the layout editor, removes selected text or items and places them on the clipboard. Copy Used to duplicate items in the layout editor, or to export graphs from a graph window. If the current graph is a histogram, then a second item is also placed on the clipboard: the columnar histogram data in text mode, which you can paste into a spreadsheet. Also see the page on copying graphics to other programs. Copy with gates (Cmd-Option-C) This is a variation on the Copy command that also copies the child gates as part of the picture put on the clipboard. Copy Samples as Text This is another variation on the Copy command that uses the clipboard to export a textual description of the selected populations and statistics. Useful for taking the sample list out to a word processor. Paste Used to duplicate items in the layout editor, to add text to a layout or when editing text fields. Inserts the contents of the clipboard into the active selection. Clear Currently disabled, except when editing text fields. Select All Select all items in the current window--all samples in the workspace window, all gates in the graph window, or all items in the layout view. Select Equivalent Nodes (Option-Command-A) Select all nodes in the workspace that are "equivalent" to the currently selected nodes. "Equivalent" means the same gating hierarchy. This way you can quickly select, for example, all of the "CD4" gates for all samples. Select every.... Selects every other, third, fourth, fifth sample etc. based on the value chosen from the popup menu. This can be useful with regular protocols where, for example, every fourth tube is stained with the same reagent. Being able to select by interval is convenient for dragging several regularly spaced samples to a group. Preferences... Set a variety of default program behaviors. Brings up the Preferences dialog window. Start / Stop Monitoring Tasks There are many operations involved in creating complex analyses. They are scheduled to take place in the background, and not tie up the computer while you want to work. These monitor windows show you if there is work on the queue, and how much longer it will take. Use this menu item to show or hide the monitor windows. Workspace menu Show Workspace Brings the workspace window to the front. Show/Hide Statistics Hides (or shows) all statistics "nodes" in the workspace. Edit Workspace Columns... Brings up a dialog to change the information displayed in the sample list of the workspace window. Sort Sample List... Brings up a dialog that lets you sort the sample list by a variety of keys. Set Annotation... Presents an edit field to change the annotation of nodes in the workspace window. Add Keyword... Adds an additional keyword to the sample's record in the workspace, for additional annotation. Note that this does not alter the FCS file, but only creates the keyword within the scope of the current workspace. To permanently and universally add the keyword, you should use ProJo. Copy Value to Group This takes the value in the currently selected field, and applies it to all of the samples in the current group. This is useful for creating keywords with a value shared by all of the members of a group. Add Samples Add FCS files to the current workspace. New Group... Create a new grouping of samples. Brings up the "Group Definition" dialog. Put into new Group... (Option-command-G) Creates a Recalculate This command asks FlowJo to compute all statistics and frequencies for the populations that are selected. In addition, all descendants of selected populations will also be recalculated. Clear & Recalculate (Option-command-=) This forces FlowJo to recompute all statistics for all populations, whether or not they have previously been computed. Compensate... Define or apply a compensation matrix. This menu item has a hierarchical list of Compensation Menu Items. If the last selection was a group, then all samples in that group are compensated; otherwise, only the selected sample is compensated. Derive Parameters... Derive new computed parameters or copy the derived parameters from a sample to other samples. This menu item has a hierarchical list of Derived Parameter Menu Items. You can only add derived parameters to a single sample; you can only copy derived parameters from a single sample that has them defined. Define Calibration... Launches the Calibration Platform that you can use to create calibrated parameters (such as absolute number of molecules per cell.) Kinetics Platform Launch the Kinetics Platform to perform time-dependent analyses. Cell Cycle Platform Launch the Cell Cycle Platform to perform DNA analyses. Population Comparison Platform... Launch the Comparison Platform to quantitate the difference between two different population distributions. The comparison platform has options for both univariate and multivariate comparisons. Multi-sample Compare... Perform a comparison between two or more different samples, ordering them based on an increasing difference from one or more control samples. Proliferation Platform Launch the Proliferation Platform used in conjunction with cellular markers to study the rate of cell replication. Recalculate (Cmd-=) Forces the computation of unresolved gates and statistics in the selected samples or groups. This is only necessary if the workspace preference regarding recalculation is set to "only if necessary" or "only if sample loaded." Clear and Recalculate (Option-Cmd-=)
Unify analyses... Makes the selected gates identical (to the group's version of the gate). If the last selected item was a group, then all samples' versions of the selected gates are made equivalent; if the last selected item was in the sample list, then only the selected gates in the sample list are unified with their counterparts from the group. Learn more about groups. Select all group samples. Selects every sample in the current sample list. Select equivalent nodes... Selects the nodes in all other samples which are equivalent to the nodes currently selected. This may be a useful prelude to opening all of those graphs (select them all, then double click on one of them). Rename... Renames a currently-selected population or group. Get Sample Info Get information about the current sample, including keywords & keyword values, compensation matrix, etc. Export... Export the raw gated data; for single sample exports, you can choose which parameters to select. Learn more about exporting raw data. Graph Info... Shows the floating graph specification window, which provides all the tools you need to change a graph to whatever characteristics you desire, and provides various gating tools. For more information, see the pages about this window. Graph Type A hierarchical menu, from which you can select one of the following six options to apply to the current graph. By holding down the option key, the type will be changed for all graph windows that are currently open. The following are the types you can select: ...Contour Plot Makes the current graph a probability contour plot. (Holding down Option while selecting this item causes all graphs that are currently open into contour plots). ...Density Plot Makes the current graph a density plot. (Holding down Option while selecting this item causes all graphs that are currently open into density plot graphs). ...Pseudo-color Plot Makes the current graph a pseudo-color plot. (Holding down Option while selecting this item causes all graphs that are currently open into dot plot graphs). ...Dot Plot Makes the current graph a dot plot. (Holding down Option while selecting this item causes all graphs that are currently open into dot plot graphs). ...Histogram Makes the current graph a histogram of whatever parameter is on the X axis. ...CDF Makes the current graph a CDF (cumulative display function) of whatever parameter is on the X axis. A CDF is the integral of a histogram. Graph options A hierarchical menu, from which you can select one of the following five options to apply to the current graph. By holding down the option key, the type will be changed for all graph windows that are currently open. The following options can be selected: ...Contour Levels... For a contour plot, select the frequency of levels that are displayed. ...Smooth When on, the data is smoothed. Affects only contour, density, and histogram plots. ...Show Outliers Draws dots for all events outside of the outermost contour in contour or density plots. ...High Resolution When on, data is calculated at higher resolution. Requires more compute time; affects only contour, density, pseudo-color, and histogram plots. ...Invert Reverse the color of the current plot. Transpose axes Switch the X and Y axes of the current plot. Select All Gates Selects all gates in the current graph window. Manually enter gate... Brings up a dialog allowing you specify a new gate in terms of channels, absolute fluorescence, or percentile within a distribution. Show Histograms... Display a histogram of every channel in the current sample for the eve Open other samples... Opens the equivalent graph of the same population for every other sample in the current group. If the windows are already open, then it changes the graph in that window to appear identical to the one you are looking at. If you hold down the option key while selecting this item, FlowJo will not ask you to confirm the operation. Change other graphs... Changes every other open graph to look like the one you are examining (i.e., FlowJo attempts to set the axes to the same channels, and the graph type and options identical to the current plot). If you hold down the option key while selecting this item, FlowJo will not ask you to confirm the operation. Next Sample Finds the next sample in the workspace sample list which has exactly the same gate as the current graph, and displays it in the current window. By holding down the option key, all graphs that are open will cycle in this way. Previous Sample Finds the previous sample in the workspace sample list which has exactly the same gate as the current graph, and displays it in the current window. By holding down the option key, all graphs that are open will cycle in this way. All graphs: Next Sample Equivalent to giving the Next Sample command to all open graphs. All graphs: Previous Sample Equivalent to giving the Previous Sample command to all open graphs. Make Movie... Turn the current graph into a QuickTime movie, using either time or another parameter to control the plot. See the Movie Platform for more information. Copy Table... Copies tabulated information from within Cell Cycle and Kinetics platform windows. The table is copied onto the clipboard, from which it can be pasted into any spreadsheet or word processor application. Layout menu Iteration Options… Brings up the dialog box allowing you to change the iteration variable, to support complex multi-sample reports. More information is available in the Layouts section. Get Info… Brings up the dialog to edit the attributes of any object in the layout. This may be line weights and colors of an arrow or box, or the axes or smoothing algorithm in a graph. Save Layout Settings Stores a copy of your layout's tiling settings back into the layout editor's list, so that that future layouts made with this template will default to the same settings. This command is only enabled for the Stack Viewer Window. Save Settings as Default (Option Key Down) Takes the current layout settings and makes it the default used when new layouts are created. Bring To Front Operates on the selected object(s) in the layout. Causes it to be drawn on top of other items. Move Up Operates on the selected object(s) in the layout. Moves the selected items one step higher in the draw order. Move Down Operates on the selected object(s) in the layout. Moves the selected items one step lower in the draw order. Send To Back Operates on the selected object(s) in the layout. Moves the selected items to the back of the draw order, causing others to be drawn on top these. Insert Picture... Provides a dialog box for you to choose any file of one of the major graphics formats: PICT, GIF, TIFF, or JPEG. Conversion of graphics formats may require either QuickTime, Clip2Gif or other plug-in translator. Group Multiple objects can be combined or "grouped" to so that they can repositioned, duplicated or deleted as a set. Select two or more items and invoke the Group command and they will be handled as a single object. Ungroup Redivide the elements of a group into individual items again. Put into Grid / Ungrid Grids are an advanced form of groups which also determine the positioning and size of objects. As a grid is resized, the spacing and sizing of the elements behaves consistently across all of the cells in the grid. More on grids. Get Grid Info... If a grid is currently selected, the Get Info... command will give you the dialog to set the attributes of the contents of the selected cell. Use this function call the Get Info... dialog for the attributes of the grid. Zoom In Increases the magnification level, so that objects are drawn larger. More controls of the layout's magnification are found in the bottom left corners of the layout windows. Zoom Out Decreases the magnification level, so that objects are drawn smaller. Magnification levels range from twice normal size to one eighth of normal size. More controls of the layout's magnification are found in the bottom left corners of the layout windows. Align… Invokes the custom alignment dialog, which will facilitate you in building publication quality layouts. The Alignment commands are not enabled unless two or more items are currently selected in the layout. Align Horizontal This item shows the submenu which contains the commands for four different ways of aligning the horizontal component of a set of layout options: by left edge, by right edge, by the center, or such that centers are equidistantly distributed between the leftmost and rightmost objects' current positions. Distribute Horizontally This command will move the objects horizontally so as to even the spaces between their outer edges. Whereas the align commands will move the horizontal position so that all objects coincide, the distribute command will spread them out to cover the space defined by the outermost objects. Align Vertical Holds the submenu which contains four alignment commands governing the vertical component of a set of layout options: by top edge, by bottom edge, by the vertical center, or such that centers are spaced evenly top to bottom. Distribute Vertically This command will move the objects up and down to even the spaces between their outer edges. Whereas the align commands will move the vertical position so that all objects coincide, the distribute command will spread them out to cover the space defined by the outermost objects. Windows Menu Table Editor... Define or create a new table of statistics. Brings up the Table Editor dialog window. Layout Editor... Define or create a new layout for graphics presentation. Brings up the Layout Editor dialog window Other Items In the Windows Menu The names of each of your documents and work windows are added to this menu, each time a new window is created. This can be used as a navigation tool, to be able to bring you back to a desired window, after it has been covered or obscured by other windows. |
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new group from the currently selected samples, putting them into the 
nts shown in the current plot.
