Fig. 4

M1/M2 dichotomy fails to classify microglial subclusters after ischemia. A Median correlation plot showing M1 polarization score and M2 polarization score of microglia from sham group and MCAO (3-h, 12-h, and 3-day post stroke) group using Corscatter (Additional file 2: Table S9). M1 polarization score and M2 polarization score of microglia from sham group and MCAO (3-h, 12-h, and 3-day post stroke) group were depicted in the box plot. B Gene score feature plot using M1-microglial marker. C Gene score feature plot using M2-microglial marker genes. D Median correlation plot showing M1 polarization score and M2 polarization score of IPAM and ICAM using Corscatter. E Median correlation plot showing the alterations of M1 polarization score and M2 polarization score in IPAM among different groups (sham, MCAO-3 h, MCAO-12 h, and MCAO-3d). F Median correlation plot showing the differences of M1 polarization score and M2 polarization score in ICAM among different groups (sham, MCAO-3 h, MCAO-12 h, and MCAO-3d). G Pseudo-time trajectory diagram of microglia. The expression of M1/ M2 microglial marker genes was depicted in the diagram respectively. H t-SNE projections highlighting M1-marker (Cd86 and Fcgr4) and M2-marker (Arg1 and Mrc1)