Population Table
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This panel contains all populations that you can make from different sources such as , , , .
Change visibility
Assign a color
You can change population color and crosses will be colored by new color. All overlaped cells are colored by color of Overlapping population. Color of each population should be unique.
Assign a name
You can change population name by clicking on corresponding table cell. Empty and duplicate names are forbidden. You can't rename Overlapping population.
You can toggle color scaling. There are two available options:
By dataset:
This option is selected by default and it means that all population intensities are normalized using 1% and 99% values of the whole dataset.
For example, the whole dataset contains 100 000 cells, so it means that all 100 000 values will be used for the intensity normalization. In this case, the intensity of a population for some marker will be Red if the median value of this population higher than the value in 99% of cells.
By populations:
if we want to compare populations with each other, then we can select this option. In this case, we will always have the lowest (blue) and the highest (red) intensities for each marker.
For example, we have 30 populations in the Population table, so it means that 30 median values of these populations will be used for the intensity normalization. In this case, the intensity of a population for some marker will be Red if the median value of this population higher than the median value in 99% of populations.
You can perform actions on multiple populations. You can select a few populations and then right click. There will be popup menu with next available actions:
Density heatmap – highlighted populations will appear in population density heatmap
Delete all - all populations will be deleted from the table.
Change color - you will be able to specify color that will be applied to all selected populations.
Toggle visibility - visibility of all selected populations will be toggled.
Combine populations - populations will be combined into new one that will have color of population with greater amount of cells.
Intersection - new population, with only intersecting cells, will be added to the table.
Set difference - new population, with cells from A without cells from B, will be created. You will be able to specify A and B in the new dialog.
Disjunctive union - new population, with all cells, except intersecting, will be added to the table.
Archive/Unarchive.
You can select multiple populations by mouse, right-click and choose 'Archive' option. Then these populations will become not visible in the table, if 'Show archived' checkbox is not selected.
When you will select 'Show archived' checkbox, all archived populations will become visible in the table (gray font). You will be able to select them, right click and choose 'Unarchive' option.
Spatial analysis
1.5 features:
The users can click on the 'Move to the Gating tab' button to move the Populations table to the Gating tab. This allows the users to work with the Populations and Gating windows without switching the tabs.
Each population contains a set of cells. You can see # of cells in corresponding column of population table. There is one population called 'Overlapping population', it represents set of cells that belong to many populations. Also you can see heat map for each population that represents median values, colored by heatmap color scheme (see ), for each marker that is selected in Marker manager.
If population is selected and is visible then you can see crosses on that highlight cells from this population. Also you can change visibility of Overlapping population, if it is not visible then all overlapped cells will be invisible.
If you want to delete population then you should click on the 'trash' button. Then this population will be removed from the table and . You can always return this population via .
If you want to see then you should select populations by mouse in table and click on the 'Cluster populations' button. Then these populations will be clustered by hierarchical algorithm and you will see row and column dendrograms.
If you want to export populations then you should select them by mouse in table and click on the 'Export' button. Then if you don't have you will see dialog where you should give a name to analysis state. Then you will see success message that populations were exported to the . In addition to FCS, populations will also be exported to CSV files.
Gate populations - all cells from selected populations will be passed to the new plot.
You can run '' activity and in this case, only cells from the selected populations will be taken.
