plotting-gene-expression

name	plotting-gene-expression
description	Generate violin plots and dot plots for gene expression visualization across cell clusters.
allowed-tools	Read, Bash
compatibility	scRNA-seq, snRNA-seq

Gene Expression Plots

When to Use

During marker gene validation and cell type annotation review.

Functions

violin_plot(adata, genes, groupby, output_dir=None) -> str

Creates violin plot showing expression distribution of specified genes across groups. Saves to {output_dir}/violin_{groupby}.png

dot_plot(adata, genes, groupby, output_dir=None) -> str

Creates dot plot showing average expression and fraction of cells expressing each gene per group. Dot size = fraction of cells expressing gene. Dot color = average expression level. Saves to {output_dir}/dotplot_{groupby}.png