Extended Data Fig. 7: slide-DNA-seq clonal analysis workflow.
From: Spatial genomics enables multi-modal study of clonal heterogeneity in tissues
a, Principal components calculated from smoothed slide-DNA-seq beads, ordered by the percentage of variance explained for the mouse liver metastases array shown in Fig. 1. b, Weights per 1 Mb genomic bin for principal components 1 and 2. Red points indicate bins from chromosomes with an odd number, blue from chromosomes with an even number (and chrX). c, slide-DNA-seq array for the mouse liver metastases array shown in Fig. 1 with points colored by raw PC 1 scores (top left), smoothed PC 1 scores (top right), raw PC 2 scores (bottom left), smoothed PC 2 scores (bottom right). d, Calinski-Harabasz criterion values used to select the optimal value of k for k-means clustering. e, slide-DNA-seq array colored by cluster assignment using the value of k selected in d. f–j, Same as a–e, but for the mouse liver metastases array shown in Fig. 2.
