Fig. 4: SiGra enhances the single-cell spatial data of Vizgen MERSCOPE.
From: SiGra: single-cell spatial elucidation through an image-augmented graph transformer
a Spatial visualization of the cell clusters in the single-cell spatial data from mouse liver tissue. b Spatial visualization of the raw expression and the enhanced expression of liver-related genes (Cyp2c38, Axin2, Cd34). c UMAP visualization of the raw expression and the enhanced expression of liver-related genes (Cyp2c38, Axin2, Cd34). d Boxplots of the raw expression and the enhanced expression of liver-specific genes in different cell clusters (C1: 63,300; C2: 44,173; C3: 39,823; C4: 29,170; Other: 190,645). In the boxplot, the centreline, box limits and whiskers denote the median, upper and lower quartiles, and 1.5× interquartile range, respectively. e Comparisons of the number of differentially expressed genes (DEGs) in cell clusters. The labelled number is the average logFC for that cell cluster. f Scatter plot of significantly associated ligand‒receptor (L-R) pairs in the raw data and the enhanced data. Orange- and yellow-coloured dots represent the shared and specific L-R pairs, respectively. Source data are provided as a Source Data file.
