search

SofieVG / FlowSOM

Using self-organizing maps for visualization and interpretation of cytometry data
61 stars 26 forks source link

PlotStars met: MST=2, plot grid option #3

Closed anaraserikbek closed 6 years ago

anaraserikbek commented 8 years ago

When using PlotStars of FlowSOM and using MST=2, what does each grid of 10x10 represent? Why, even if the number of markers change, the grid size stays the same. Could you maybe give some reading on how exactly the tree is build & maybe some reading about the algorithm? Thank you

SofieVG commented 8 years ago

The nodes of the grid do not correspond to the markers: every node is a cluster of similar cells (so each node will have the amount of markers you defined, which can be shown in a star plot). You can vary the number of nodes in the grid by using the xdim and ydim parameters of the functions FlowSOM or BuildSOM. If the number of nodes (= xdim * ydim) is too low, not all populations of interest will be splitted into separate nodes, but if the number is too high, the figures can become cluttered. In general, I work with a 7x7 grid (49 clusters), except when I know I'm looking for a rare population, when I use a 10x10 grid (100 clusters). Sometimes the occasion may ask for a different number of nodes, but this happens very rarely in my experience. You can find our publication here: http://onlinelibrary.wiley.com/doi/10.1002/cyto.a.22625/abstract