Documentation

Plots

When a new file is opened for the first time a dot plot is displayed for it. By default Floreada tries to display FCS/SSC on X/Y axis if possible. Parameters in FCS files are given two names, a short name and a long name. These names are stored in two keywords $PnN and $PnS, where "n" is the parameter number. Floreada will display the full parameter name as "Long Name" :: "Short Name" unless the two are the same and then it will just display it once. Currently all dot plots are displayed in color representing the event density with blue being least dense, then green, then yellow, and finally red being most dense.

Select Parameters

In order to change parameters, click on the current x or y parameter name. A popup menu will display with all the currently available parameter names, where you can select the new parameter for the axis.

Set Axis

To change the current axis, click on the axis and a popup will display. A histogram is shown to help you visualize the distribution of events as you change the scale. You can adjust the minimum and maximum axis values as well as switch between the follow scale types:

Logicle is a special transformation developed at Stanford. It puts events near zero on a linear scale and bigger events on a log scale. It helps to spread out big groups of events around zero, which can be a problem if you vizualize data on a logarithmic scale. Another plus of Logicle is that unlike regular Logarithmic scaling, it is defined for negative events. Some FCS files do contain negative data and events may become negative if compensated as well. If these are displayed on a regular log scale, they will be ignored. But Logicle can evaluate and display negative events.

There are several parameters that you can set when specifying a new Locigle transform:

Floreada will fill in sane settings to start with but you can change any value you want to.

Changing Point Size

The size of the points of a plot can be adjusted. Right click on the plot and under the "Point Size" menu option, you can select from several possible sizes.

Download Plot Image

If you would like to save the current plot image, click "File" then "Save Image". You can select from a bunch of different options, and can enable or disable multiple different aspects of the current plot from appearing in the image, such as the plot title, the axis label, etc. You can also customize the displayed X and Y axis labels if needed.

Currently images are saved as PNG files but we can add more file types if needed. There is also a batch option that can be applied. If you check this box, the comparable images for all files in the project will be exported in a zip file. For instance, if you are exporting the image for a population based of a "Lymphocyte" gate which you have created. All other files that have that same gating structure will also have their comparable image exported as well.