Fig. 2

MetaPop Visualization Outputs from our autism biological virome dataset. Pre-processing visualizations include a bar plot showing how many reads were kept and removed following removal of reads below a 95% ID cut-off across all samples, b scatter and bar plot composites (1 example shown) reported per sample showing how many genomes pass the horizontal and vertical coverage cut-offs, and (b—inset) donut plots summarizing the total number of genomes passing the different horizontal and vertical coverage cut-offs per sample. Macrodiversity visualizations include a heatmap summarizing the normalized abundances of covered genomes across the different samples (the max value on the color scale reported is the 75% quantile of all abundances to allow low abundance genomes to be better displayed; another heatmap not shown is also created showing a full range of abundances), b scatter plots per each alpha diversity index (4 examples shown) showing the alpha diversity value across all samples with horizontal lines showing the mean and median values, c ordination plots (PCA, PCoA, and NMDS) of all centered-log ratio transformed Euclidean distances, Bray-Curtis distances, and Jaccard distances, respectively (all distances are plotted using the 3 ordination methods by default). The color of each circle represents the species richness within each sample. The codon usage bias visualization is a circular bar plot per genome (1 example shown) showing the Euclidean distance of each gene from the average gene codon bias. Genes with outlier codon biases are displayed in red. Microdiversity visualizations include a Stacked bar plot (right) and standard bar plot (left) showing the distribution of SNPs across codon position and the total number of SNPs per sample. bF_ST heatmaps per genome (2 examples shown) showing the population differentiation per genome across all samples it has coverage within. c Genome plot composites for each genome in each sample where it has coverage (1 example shown) with four different tracks from top to bottom showing a line graph of the depth coverage of the genome, a genome plot of the genome with coloration of genes showing pN/pS results, a scatter plot showing π and θ values, and, lastly, a scatter plot showing Tajima’s D values with the color background showing whether the value is indicative of selection