Cytosplore Viewer allows to define a few advanced (default) settings, for example for the A-tSNE computation (such as the number of iterations) and visualization options (e.g. point size for the scatter plots, highlighting mode). These defaults can be customized through the Cytosplore.ini file located in the program folder.
; lines with a preceding ; are comments [section headers] are marked with square brackets [tsne] ; the number of iterations for the A-tSNE gradient descent iterations=300 ; the A-tSNE gradient descent has three phases, in the first the forces are exaggerated to achieve quicker 'pre-sorting' of the points. exaggerationItererations sets the number of iterations for this phase exaggerationItererations=100 ; in the second phase the axagerated forces are gradually removed. exponentialDecay sets the number of iterations for this phase. The third phase resembling regular t-SNE starts after exaggerationItererations + exponentialDecay iterations. exponentialDecay=70 ; The perplexity (i.e. the local neighborhood to consider) for the A-tSNE perplexity=30 [statistics] ; the minimum number of expression values required for beta and differential mean computations minimumSizeThreshold=5 ; the minimum number of expression values required to rank-sum test rankSumThreshold=10 ; threshold value for beta computation betaValueThreshold=1.0 ; turn the progress bar on or off showProgressBar=1; [sliderSettings] ; the relative point size in the map viewer pointSize=110 ; the relative size ofthe halos around the points for highlighting in the map viewer haloSize=40 ; the opacity of the points in the map viewer (0% to 100%) pointOpacity=60 ; toggle for different modes of the 'hide selection' toggle hideSelection=0 [hierarchy] ; the number of beta and differential expression values shown in the hierarchy view per cluster nrOfExpressions=10