Fig. 1
From: GECO: gene expression clustering optimization app for non-linear data visualization of patterns
GECO app interface to generate reduced date. Once a data matrix is uploaded in the main window and samples are identified, this side bar is used to select the desired reduction type (t-SNE or UMAP). Normalization options include default settings of removing entries with all zeros and row normalization. Normalizing to a selected type is optional. Parameter options for t-SNE include initial PCA reduction, perplexity, learning rate, early exaggeration, and iteration number. UMAP parameters include number of neighbors, minimum distance, and distance metric. Standard default settings automatically appear, but links to t-SNE and UMAP parameter guides are provided to aid in exploration and customization