Statistical & expression visualizations

These charts are the workhorses of transcriptomic and comparative analysis. Most are generated automatically when EMET runs differential expression or retrieves multi-sample data.

Volcano Plot

Log2 fold change vs. −log10 p-value. Highlights significantly up/down-regulated genes in red and blue.

Triggered by: DESeq2 / differential expression results

Heatmap

Color-coded matrix for gene × sample expression, correlation matrices, or drug response profiling. Supports hierarchical clustering.

Triggered by: multi-gene expression tables, correlation data

PCA Plot

Principal component analysis scatter — reveals batch effects, outliers, and group separation in multi-sample datasets.

Triggered by: DESeq2 QC, multi-sample expression analysis

Box Plot

Median, quartiles, and outliers across groups — comparing distributions by condition, tissue, or mutation status.

Ask: "Show the distribution of expression by group"

Bar Chart

Categorical comparisons — expression by tissue, mutation counts by type, drug response by cell line.

Ask: "Show expression across these tissues as a bar chart"

MA Plot

Average expression vs. log fold change — detects expression-dependent bias after differential expression analysis.

Triggered by: DEG QC workflow

Scatter Plot

Two-variable correlation, clustering, or x-y relationships. Supports trendlines and group coloring.

Ask: "Scatter plot of X vs Y" or "Show the correlation"

Histogram

Distribution of continuous values — allele frequencies (VAF), expression distributions, PHRED quality scores.

Ask: "Show the distribution of variant allele frequencies"

Line Chart

Temporal trends or sequential data — time-course expression, drug concentration over time, longitudinal measurements.

Ask: "Plot expression over time"