Average cell scores of macrophage neighborhoods ( n = 858) enriched in non-responders under therapy and cell scores for all other macrophage neighborhoods in the independent Bassez and Zhang breast cancer datasets. Cell scores were calculated using the Spectra invasion factor (factor 182 from Bassez et al. 10 ) or by using scanpy.score_genes 1 , 2 on the top 50 marker genes of factor 182 in Zhang et al. 23 . P values (two-sided) were calculated using Mann–Whitney U- tests (Bassez: P = 4.96 x 10 –5 , statistic = 1,060, Cohen’s d = 1.49; Zhang: P = 3.74 x 10 –12 , statistic = 600,886, Cohen’s d = 1.03). Boxes and lines represent IQR and median, respectively; whiskers represent 1.5x IQR.
