Fig. 4

The human prostate cancer dataset was downloaded from \(10\times\) Genomics website. 10x Genomics website. The tissue was stained by immunofluorescence using antibodies Iba1/AIF-1 (green),Vimentin (red), DAPI (blue) (A). Data were normalized using Seurat [1], exported and Hallmark pathways were scored using Single-cell Explorer Scorer [8]. Using Single-Cell Spatial Explorer, scores from hallmark pathways (hypoxia, left; Androgen Response right) are visualized (B). C On the “Hypoxia”/“Androgen Response” dot plot, spots were selected (Hypoxia\(^+\)AndrogenResponse\(^-\) in pink and Hypoxia\(^-\)AndrogenResponse\(^+\) in yellow) and visualized on the tissue image. D Area from the tissue image were selected and spots from this area were visualized on the “Hypoxia”/“Androgen Response ” dot plot (top) or compared using all the hallmark pathways resulting in a table and a volcano plot (E). Interesting dot can be selected (red circle in E) and the corresponding data visualized on the tissue image (F)