2.12 Immune cell infiltration and correlation analysis

The CIBERSORT (http://cibersort.stanford.edu/) (20) algorithm was used to quantify the content of infiltrated immune cells between OA and normal cartilage. We used the “corrplot” R package to analyze and visualize the relationship of the 22 infiltrated immune cells. We applied the “vioplot” R package to represent the variations of infiltrated immune cells between normal and OA cartilage samples with violin plots. Spearman’s rank correlation was conducted to clarify the correlation between infiltrated immune cell levels and PDK1 expression in different samples. Finally, the “ggplot2” R package was applied to visualize the associations.