Figure S5.
Validation of parameters for scRNA-seq analysis of CD4+ T cells. Related to Figs. 1, 2, 3, and 4. (a–d) Related to Figs. 1 and 2. Degree of overlap measured by adjusted Rand index between Phenograph clustering in gp66:I-Ab+ CD4+ T cell replicates with varying input number of PCs (a and b) and k (c and d). (e–h) Related to Fig. 3. Validation of imputation and diffusion mapping for C7 differentiation during acute L.m.-ESAT infection. Average Pearson correlation per gene of MAGIC imputed expression values with varying input ka (e) and t parameters (f). (g) Average Pearson correlation distance per gene between successive applications of the MAGIC diffusion operator indicated by t. (h) Pearson correlation in cell–cell diffusion distances calculated for C7 differentiation dataset with varying numbers of diffusion components (DCs). (i–k) Related to Fig. 4. Validation of naïve CD4+ T cell batch-correction, clustering, and imputation. (i) Heatmap showing the overlap coefficient of DEGs recovered in each individual replicate sample after Phenograph clustering (20PCs, k = 30) followed by one-vs-rest cluster comparisons performed with MAST (log2FC > 0.5, FDR < 1e-10). (j) Heatmap showing the degree of overlap measured by the adjusted Rand index between clustering in individual samples using varying numbers of HVGs as compared with clustering in individual samples using all expressed genes. (k) Pearson correlation between average cluster expression profiles calculated separately in each individual sample. Colored bars at the top and sideshow the collective Phenograph clustering assignment of each profile. (l–p) Related to Fig. 4. Validation of clustering and imputation for naïve CD4+ T cell dataset. (l and m) Degree of overlap measured by adjusted Rand index between Phenograph clustering on the combined batch-corrected naïve T cell dataset with varying input number of PCs (l) and k (m). (n and o) Average Pearson correlation per gene of MAGIC imputed expression values with varying input ka (n) and t (o) parameters. (p) Average Pearson correlation distance per gene between successive applications of the MAGIC diffusion operator indicated by t.

Validation of parameters for scRNA-seq analysis of CD4+ T cells . Related to Figs. 1, 2, 3, and 4. (a–d) Related to Figs. 1 and 2. Degree of overlap measured by adjusted Rand index between Phenograph clustering in gp66:I-Ab+ CD4+ T cell replicates with varying input number of PCs (a and b) and k (c and d). (e–h) Related to Fig. 3. Validation of imputation and diffusion mapping for C7 differentiation during acute L.m.-ESAT infection. Average Pearson correlation per gene of MAGIC imputed expression values with varying input ka (e) and t parameters (f). (g) Average Pearson correlation distance per gene between successive applications of the MAGIC diffusion operator indicated by t. (h) Pearson correlation in cell–cell diffusion distances calculated for C7 differentiation dataset with varying numbers of diffusion components (DCs). (i–k) Related to Fig. 4. Validation of naïve CD4+ T cell batch-correction, clustering, and imputation. (i) Heatmap showing the overlap coefficient of DEGs recovered in each individual replicate sample after Phenograph clustering (20PCs, k = 30) followed by one-vs-rest cluster comparisons performed with MAST (log2FC > 0.5, FDR < 1e-10). (j) Heatmap showing the degree of overlap measured by the adjusted Rand index between clustering in individual samples using varying numbers of HVGs as compared with clustering in individual samples using all expressed genes. (k) Pearson correlation between average cluster expression profiles calculated separately in each individual sample. Colored bars at the top and sideshow the collective Phenograph clustering assignment of each profile. (l–p) Related to Fig. 4. Validation of clustering and imputation for naïve CD4+ T cell dataset. (l and m) Degree of overlap measured by adjusted Rand index between Phenograph clustering on the combined batch-corrected naïve T cell dataset with varying input number of PCs (l) and k (m). (n and o) Average Pearson correlation per gene of MAGIC imputed expression values with varying input ka (n) and t (o) parameters. (p) Average Pearson correlation distance per gene between successive applications of the MAGIC diffusion operator indicated by t.

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