Fig. 5: HEARTSVG identifies cell type-specific marker genes with distinct spatial patterns across different MERFISH datasets. | Nature Communications

Fig. 5: HEARTSVG identifies cell type-specific marker genes with distinct spatial patterns across different MERFISH datasets.

From: HEARTSVG: a fast and accurate method for identifying spatially variable genes in large-scale spatial transcriptomics

Fig. 5

a Visualization of known cell annotations of the MERFISH data 1 (6,112 cells with 155 genes). b Visualization of unsupervised spatial clustering results of the MERFISH data 2 (5665 cells with 156 genes and 5 blank controls). c Venn diagrams of SVGs identified by HEARTSVG, SpatialDE, SPARK, SPARK-X, scGCO and Squidpy. d Visualizations of representative marker genes for ependymal, excitatory, and oligodendrocyte cell types, along with corresponding adjusted p-values obtained by HEARTSVG in two MERFISH datasets. P-values were calculated by HEARTSVG, and adjusted using Holm’s method. The panels above of Fig. 5c and Fig. 5d correspond to the MERFISH data 1. The panels below correspond to the MERFISH data 2. Source data are provided with this paper.

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