This can be accessed by right clicking on a graph and selecting properties, or double clicking the plot. To edit the fields that appear by default, use the Annotation preferences.Īnnotations can also be toggled on or off through the Graph Definition window. By default, the size of the box is fixed, so it is advisable to make this box a little wider than may seem necessary, and check reports to make sure text or statistics are not being truncated.ĭragging statistics to the layout editor or using the Text tool will also create FMJL fields. A checkbox to Resize box to fit text will determine whether changes in the text coming from looking at different samples will cause the box to resize itself. The line fill weight, style and color of the box enclosing Annotation can be changed here. The compensation matrix was calculated in Flowjo. Figure 3: Beads were stained with antibodies and acquired on a FACSCanto-II. The instrument was under tight control, and the voltages based on application-specific settings, coupled with using peak 6 beads to check voltage. Keywords and other information can be added to the Annotation display by selecting any of the keywords associated with your FCS file by selecting from the Insert Keyword.įonts can be customized in the Object tab of the Layout Editor. Figure 3 shows how a compensation matrix acquired one week apart change. The text box at the top uses our own markup language, FJML, to give you the ability to mix text and data. We generated a compensation matrix at both gain settings. The test is performed at two different gains settings, see Table 1. Alternatively, you can control-click (Mac)/ right-click (PC) to invoke the annotation drop down menu. Double clicking on a field, or choosing “Insert FJML” from the drop-down menu will produce the dialog window shown below. At the bottom you see the option to insert a keyword or annotation. In order to demonstrate the Gain Independent Compensation function, we compare the results from different scenarios in figure 3. To edit an individual Annotation, double-click on annotation object and you will see the fields within the annotation box outlined in green. ![]() In the figure below, new annotations are indicated in bold red text, the default annotations are in black. For instance, you might want to include the compensation matrix you used to generate a particular report, the date the experiment was done, and add your own text noting problems or experimental specifics. To familiarize yourself with this interface, read this chapter.Add Annotations to your graphical reports in FlowJo to save time avoiding time-consuming searches through notebooks for experimental details.Īn Annotation automatically appears when plots are a dropped into the Layout Editor.Īdding annotations to graphical reports is useful for recalling certain aspects of a report and when sharing reports with others. Once you have a compensation matrix and wish to examine it, you will be using the Matrix Editor. If you acquired your data with single-stain controls and wish to compensate it using FlowJo, read this chapter. CHAPTER 2 – Creating a FlowJo compensation matrix from single stain controls If, for any reason, you want to alter the matrix values, read this chapter. This keyword is read and data in the file are compensated when the data is read into FlowJo. Many data files contain their own pre-defined compensation matrix keyword, which was written when the file was created. CHAPTER 1 – Altering an acquisition matrix Poorly scaled data will effect downstream compensation, so get into the habit of adjusting transforms through the “T” button in FlowJo’s graph window, prior to opening the compensation wizard for single stained control assignment. To demonstrate the effect of gate placement I’m using FlowJo’s automated compensation tool, though this should be applicable to any comparable software. Note, Compensation should always be preceded by scaling your data appropriately. For your convenience, this document is broken into chapters. ![]() This page will help acquaint you with the various ways to interact with Compensation Matrices in FlowJo.
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