Abstract The rapid development of scRNA-seq technologies enables us to explore the transcriptome at the cell level in a large scale. Recently, various computational methods have been developed to analyze the scR-NAseq data such as clustering and visualization. However, current visualization methods including t-SNE and UMAP are challenged by the limited accuracy of rendering the geometic relationship of populations with distinct functional states. Most visualization methods are unsupervised, leaving out information from the clustering results or given labels. This leads to the inaccurate depiction of the distances between the bona fide functional states and the variance of clusters. We present supCPM, a robust supervised visualization method, which separates different clusters, preserves global structure, and tracks the cluster variance. Compared with six visualization methods using synthetic and real data sets, supCPM shows improved performance than other methods in preserving the global geometric structure and data variance. Overall, supCPM provides an enhanced visualization pipeline to assist the interpretation of functional transition and accurately depict population segregation.