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Target Density Downsampling

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Target Density downsampling is a method to discard events based on their local density. Please read our introduction to sampling if you have not done so already to learn about your options for calculating local density.

Target density downsampling is implemented as originally described in Qui, P et. al. "Extracting a Cellular Hierarchy from High-dimensional Cytometry Data with SPADE", Nature Biotechnology, 29(10):886-891, 2011. The goal is to ensure that the final density of the sampled population falls within a certain density range. Events with local densities below the desired density range are discarded. Events with the local densities within the desired range are kept. Events with local densities above the desired range with are discarded with a probability that depends on how much the local density is greater than the desired range. The higher the local density is compared to the desired range, the more likely it is to be discarded.

Target Density Downsampling has several options

Specify Density Percentiles	By default the option is checked, and the user can define how the density-dependent downsampling is performed by entering Min Density and Target Density values. If the box is unchecked, Sample Size may be defined instead of these two values.
Min Density	If the local density of a cell is less than the Min Density value, it will be excluded from sampling. Values range from 0 to 1. Default is 0.01.
Target Density	If the local density of a cell is greater than the Min Density percentile and less than the Target Density, it will be sampled. When the Local density of a cell is greater than the Target Density, it will be sampled randomly with a probability equal to the ratio of Target Density/Local density. Values range from 0 to 1. Default is 0.20.
Sample Size	Indicates how many cells to subsample when performing the transformation. This option becomes available when the Specify Density Percentiles check-box is unchecked, . If using this option, the Min Density and Target Density will be automatically estimated to select cells. If the specified Sample Size is higher than the number of available events, SPADE will be run on all available events. Note that the number of available events is dictated by the Gate option. The minimum value that can be entered is 10.