GateToolGui : gating and plotting of multiple clists
For additional clist and gating options, the gateToolGui offers more extensive options. These options are broken into the following sections of the GUI:
- Load clists : load clist(s) from directory entered in text box
- Add clist : add a clist from another folder
- Delete clist : remove the current clist from the loaded GUI clist list
- Save csv : saves you current clist as a csv so it may be used in analysis software external to matlab
- Save clist : saves your currently loaded clist to a .mat file
- First drop down menu: select clist to act on. The all option allows you to act on all clists
- Time : This checkbox allows you to use the time-dependent 3D clist rather than the regular clist
- Next two drop down menus : Select up to two cell descriptors from the clist to act on using the clist actions in the next section.
The numbers at the bottom of the panel are the number of clists loaded and their orientation. Clists oriented vertically will be treated as one clist for plotting, where as clists oriented horizontally will be treated as separate clists.
- Delete gate : removes all gates from the selected clist(s)
- Strip gated cells : remove cells from the clist which do not fall within gates
- Squeeze : treats several loaded clists as a single data set by making them a vertical set of clists (without actually combining the clists)
- Expand : when clists have been squeezed, the expand option allows you to treat them as separate entries again by making them a horizontal set of clists
- Close all figures : closes all open figures
- Name a clist : add a label to the selected clists. Now when data from these clists are plotted, the legend will list them by this name.
There are three different plot types which you can make. They are:
- Histogram : this creates a 1D or 2D histogram, depending on how many cell descriptors have been selected in the "Panel" section
- Kernel density estimator : this creates a 1D or 2D smoothed histogram, using a gaussian kernel on the histogram values
- Dot plot (2D only): this creates a 2D plot with one cell descriptor on the y- and one cell descriptor on the x- axis. Dots represent data points.
- Conditional (2D only) : this modifies the plot to show the conditional probability rather than the histogram values
- Density (2D only) : this modifies the plot to show of the probability density rather than the histogram
- Errors (1D only) : shows the error on the mean of a 1D histogram
- States (1D only) : shows the mean, std, error for a 1D histogram
- Log : by checking the boxes following the Log box, you may choose to use a log scaling on the x, y, or z axes
- Show : displays the type of plot specified by above controls
- Make gate : allows you to use the generated interactive plot to select a gate