Bio De Visualization Agent Skill

Visualize differential expression results using DESeq2/edgeR built-in functions. Covers plotMA, plotDispEsts, plotCounts, plotBCV, sample distance heatmaps, and p-value histograms. Use when visualizing differential expression results.

6k tokens

context cost

the whole folder, loaded on every use

files

instructions only

copies elsewhere

how many repositories repackaged it

132

stars on the repo

on the repository, not the skill itself

Install

one command, takes just this skill from the repository

npx skills add https://github.com/BioTender-max/awesome-bio-agent-skills --skill bio-de-visualization

What comes with it

7 424 bytes besides the instruction

examples/heatmap.R

examples/pca_plot.R

examples/volcano_plot.R

usage-guide.md

The instruction itself

38 sections, as written by the author

Version Compatibility

Reference examples tested with: DESeq2 1.42+, edgeR 4.0+, ggplot2 3.5+, limma 3.58+, matplotlib 3.8+

Before using code patterns, verify installed versions match. If versions differ:

R: packageVersion('<pkg>') then ?function_name to verify parameters

If code throws ImportError, AttributeError, or TypeError, introspect the installed

package and adapt the example to match the actual API rather than retrying.

DE Visualization

Create visualizations for differential expression analysis using DESeq2 and edgeR built-in plotting functions.

Scope

This skill covers DE-specific built-in functions:

DESeq2: plotMA(), plotPCA(), plotDispEsts(), plotCounts()
edgeR: plotMD(), plotBCV(), plotMDS()
Sample distance heatmaps and p-value distributions

For custom ggplot2/matplotlib implementations of volcano and MA plots, see data-visualization/volcano-and-ma-plots; for PCA / UMAP / t-SNE / PHATE, see data-visualization/dimensionality-reduction-plots.

Required Libraries

library(DESeq2)
library(ggplot2)
library(pheatmap)
library(RColorBrewer)
library(ggrepel)  # For labeled points

Installation

install.packages(c('ggplot2', 'pheatmap', 'RColorBrewer', 'ggrepel'))
# Optional: Enhanced volcano plots
BiocManager::install('EnhancedVolcano')

MA Plot

Goal: Visualize the relationship between mean expression and log fold change to assess DE results.

Approach: Plot log fold change against mean normalized counts, highlighting significant genes.

"Make an MA plot of my DE results" → Plot mean expression vs. fold change with significant genes colored, using plotMA or ggplot2.

DESeq2 MA Plot

# Built-in MA plot
plotMA(res, ylim = c(-5, 5), main = 'MA Plot')

# With custom alpha
plotMA(res, alpha = 0.05, ylim = c(-5, 5))

# Highlight specific genes
plotMA(res, ylim = c(-5, 5))
with(subset(res, padj < 0.01 & abs(log2FoldChange) > 2),
     points(baseMean, log2FoldChange, col = 'red', pch = 20))

Custom ggplot2 MA Plot

res_df <- as.data.frame(res)
res_df$significant <- res_df$padj < 0.05 & !is.na(res_df$padj)

ggplot(res_df, aes(x = log10(baseMean), y = log2FoldChange, color = significant)) +
    geom_point(alpha = 0.5, size = 1) +
    scale_color_manual(values = c('grey60', 'red')) +
    geom_hline(yintercept = 0, linetype = 'dashed') +
    labs(x = 'log10(Mean Expression)', y = 'log2 Fold Change', title = 'MA Plot') +
    theme_bw() +
    theme(legend.position = 'bottom')

edgeR MA Plot

# Using plotMD (mean-difference plot)
plotMD(qlf, main = 'MD Plot')
abline(h = c(-1, 1), col = 'blue', lty = 2)

Volcano Plot

Goal: Display statistical significance against fold change magnitude to identify the most important DE genes.

Approach: Plot -log10(p-value) vs. log2 fold change with threshold lines and optional gene labels.

"Create a volcano plot of differentially expressed genes" → Scatter plot of fold change vs. significance with colored significance regions and labeled top hits.

Basic Volcano Plot

res_df <- as.data.frame(res)
res_df$significant <- res_df$padj < 0.05 & abs(res_df$log2FoldChange) > 1

ggplot(res_df, aes(x = log2FoldChange, y = -log10(pvalue), color = significant)) +
    geom_point(alpha = 0.5, size = 1) +
    scale_color_manual(values = c('grey60', 'red')) +
    geom_vline(xintercept = c(-1, 1), linetype = 'dashed', color = 'blue') +
    geom_hline(yintercept = -log10(0.05), linetype = 'dashed', color = 'blue') +
    labs(x = 'log2 Fold Change', y = '-log10(p-value)', title = 'Volcano Plot') +
    theme_bw()

Volcano with Gene Labels

res_df <- as.data.frame(res)
res_df$gene <- rownames(res_df)
res_df$significant <- res_df$padj < 0.05 & abs(res_df$log2FoldChange) > 1

# Label top genes
top_genes <- head(res_df[order(res_df$padj), ], 10)

ggplot(res_df, aes(x = log2FoldChange, y = -log10(pvalue))) +
    geom_point(aes(color = significant), alpha = 0.5, size = 1) +
    scale_color_manual(values = c('grey60', 'red')) +
    geom_text_repel(data = top_genes, aes(label = gene),
                    size = 3, max.overlaps = 20) +
    geom_vline(xintercept = c(-1, 1), linetype = 'dashed') +
    geom_hline(yintercept = -log10(0.05), linetype = 'dashed') +
    labs(x = 'log2 Fold Change', y = '-log10(p-value)') +
    theme_bw()

EnhancedVolcano

library(EnhancedVolcano)

EnhancedVolcano(res,
    lab = rownames(res),
    x = 'log2FoldChange',
    y = 'pvalue',
    pCutoff = 0.05,
    FCcutoff = 1,
    title = 'Differential Expression',
    subtitle = 'Treatment vs Control')

PCA Plot

Goal: Assess sample clustering and identify batch effects or outliers via dimensionality reduction.

Approach: Apply variance-stabilizing transformation then project samples onto principal components, coloring by experimental variables.

"Show me a PCA plot of my samples" → Perform PCA on transformed expression data and visualize sample separation by condition and batch.

DESeq2 PCA

# Variance stabilizing transformation first
vsd <- vst(dds, blind = FALSE)

# Basic PCA
plotPCA(vsd, intgroup = 'condition')

# With more options
plotPCA(vsd, intgroup = c('condition', 'batch'), ntop = 500)

Custom PCA with ggplot2

vsd <- vst(dds, blind = FALSE)
pca_data <- plotPCA(vsd, intgroup = c('condition', 'batch'), returnData = TRUE)
percentVar <- round(100 * attr(pca_data, 'percentVar'))

ggplot(pca_data, aes(x = PC1, y = PC2, color = condition, shape = batch)) +
    geom_point(size = 4) +
    xlab(paste0('PC1: ', percentVar[1], '% variance')) +
    ylab(paste0('PC2: ', percentVar[2], '% variance')) +
    ggtitle('PCA Plot') +
    theme_bw() +
    theme(legend.position = 'right')

edgeR PCA (via limma)

library(limma)
log_cpm <- cpm(y, log = TRUE)
plotMDS(log_cpm, col = as.numeric(group), pch = 16)
legend('topright', legend = levels(group), col = 1:nlevels(group), pch = 16)

Heatmaps

Goal: Visualize expression patterns of significant genes across samples to reveal clusters and condition effects.

Approach: Z-score normalize VST-transformed counts for significant genes and cluster with pheatmap, annotating by condition.

"Make a heatmap of the top differentially expressed genes" → Extract significant genes, z-score normalize, and create a clustered heatmap with sample annotations.

Top DE Genes Heatmap

library(pheatmap)

# Get top significant genes
sig_genes <- rownames(subset(res, padj < 0.01))

# Get normalized counts
vsd <- vst(dds, blind = FALSE)
mat <- assay(vsd)[sig_genes, ]

# Scale by row (z-score)
mat_scaled <- t(scale(t(mat)))

# Create annotation
annotation_col <- data.frame(
    condition = colData(dds)$condition,
    row.names = colnames(mat)
)

pheatmap(mat_scaled,
         annotation_col = annotation_col,
         show_rownames = FALSE,
         clustering_distance_rows = 'correlation',
         clustering_distance_cols = 'correlation',
         color = colorRampPalette(c('blue', 'white', 'red'))(100),
         main = 'Top DE Genes')

Sample Distance Heatmap

vsd <- vst(dds, blind = FALSE)

# Calculate sample distances
sampleDists <- dist(t(assay(vsd)))
sampleDistMatrix <- as.matrix(sampleDists)

# Annotation
annotation <- data.frame(
    condition = colData(dds)$condition,
    row.names = colnames(dds)
)

pheatmap(sampleDistMatrix,
         annotation_col = annotation,
         annotation_row = annotation,
         clustering_distance_rows = sampleDists,
         clustering_distance_cols = sampleDists,
         color = colorRampPalette(c('white', 'steelblue'))(100),
         main = 'Sample Distance Matrix')

Gene Expression Heatmap

# Select genes of interest
genes_of_interest <- c('gene1', 'gene2', 'gene3', 'gene4', 'gene5')
mat <- assay(vsd)[genes_of_interest, ]

pheatmap(mat,
         scale = 'row',
         annotation_col = annotation_col,
         show_rownames = TRUE,
         cluster_cols = TRUE,
         cluster_rows = TRUE,
         main = 'Genes of Interest')

Dispersion Plot

Goal: Assess the fit of the dispersion model to verify DE analysis assumptions.

Approach: Plot gene-wise, fitted, and final dispersion estimates against mean expression.

DESeq2

plotDispEsts(dds, main = 'Dispersion Estimates')

edgeR

plotBCV(y, main = 'Biological Coefficient of Variation')

Counts Plot for Individual Genes

Goal: Visualize expression of a specific gene across samples and conditions.

Approach: Extract per-sample counts for a gene and plot by condition using plotCounts or ggplot2.

DESeq2

# Plot counts for a specific gene
plotCounts(dds, gene = 'GENE_NAME', intgroup = 'condition')

# With ggplot2
d <- plotCounts(dds, gene = 'GENE_NAME', intgroup = 'condition', returnData = TRUE)
ggplot(d, aes(x = condition, y = count, color = condition)) +
    geom_point(position = position_jitter(width = 0.1), size = 3) +
    scale_y_log10() +
    ggtitle('GENE_NAME Expression') +
    theme_bw()

edgeR

# Get CPM for a gene
gene_idx <- which(rownames(y) == 'GENE_NAME')
cpm_gene <- cpm(y)[gene_idx, ]

# Plot
df <- data.frame(cpm = cpm_gene, group = group)
ggplot(df, aes(x = group, y = cpm, color = group)) +
    geom_point(position = position_jitter(width = 0.1), size = 3) +
    scale_y_log10() +
    labs(y = 'CPM', title = 'GENE_NAME Expression') +
    theme_bw()

P-value Histogram

Goal: Diagnose the quality of the DE analysis by examining the raw p-value distribution.

Approach: Histogram of raw p-values; a uniform distribution with a peak near zero indicates a well-calibrated test.

# Check p-value distribution (should be uniform under null with peak near 0)
res_df <- as.data.frame(res)
ggplot(res_df, aes(x = pvalue)) +
    geom_histogram(bins = 50, fill = 'steelblue', color = 'white') +
    labs(x = 'P-value', y = 'Frequency', title = 'P-value Distribution') +
    theme_bw()

Saving Plots

Goal: Export publication-quality plots in vector or raster formats.

Approach: Use pdf/png devices or ggsave with appropriate resolution and dimensions.

# Save as PDF (vector)
pdf('volcano_plot.pdf', width = 8, height = 6)
# ... plot code ...
dev.off()

# Save as PNG (raster)
png('volcano_plot.png', width = 800, height = 600, res = 150)
# ... plot code ...
dev.off()

# Using ggsave for ggplot objects
p <- ggplot(...) + ...
ggsave('plot.pdf', p, width = 8, height = 6)
ggsave('plot.png', p, width = 8, height = 6, dpi = 300)

Color Palettes

Goal: Select appropriate color schemes for heatmaps and categorical data.

Approach: Use RColorBrewer palettes -- diverging for expression, sequential for distances, qualitative for groups.

# For heatmaps
library(RColorBrewer)

# Diverging (for expression: blue-white-red)
colorRampPalette(rev(brewer.pal(n = 7, name = 'RdBu')))(100)

# Sequential (for distances)
colorRampPalette(brewer.pal(n = 9, name = 'Blues'))(100)

# For categorical groups
brewer.pal(n = 8, name = 'Set1')

Quick Reference: Common Plots

| Plot | Purpose | Function |

|------|---------|----------|

| MA plot | LFC vs mean expression | plotMA(), plotMD() |

| Volcano | LFC vs significance | ggplot2, EnhancedVolcano |

| PCA | Sample clustering | plotPCA(), plotMDS() |

| Heatmap | Gene patterns | pheatmap() |

| Dispersion | Model fit | plotDispEsts(), plotBCV() |

| Counts | Individual genes | plotCounts() |

Diagnostic Interpretation

P-value Histogram

Check raw p-value distribution before trusting DE results:

| Shape | Meaning | Action |

|-------|---------|--------|

| Uniform + spike near 0 | Correct: null genes uniform, true DE near 0 | Proceed normally |

| Anti-conservative (U-shape, spikes at 0 and 1) | Inflated significance; unmodeled batch or violated assumptions | Check for batch effects, verify model specification |

| Conservative (depleted near 0, spike near 1) | Over-correction; too many covariates or wrong dispersion | Simplify model, check dispersion plot |

| Spike at p = 1 only | Discrete artifact from low-count genes | Pre-filter more aggressively |

MA Plot Diagnostics

| Pattern | Meaning |

|---------|---------|

| Symmetric cloud centered at LFC = 0 | Correct normalization |

| Cloud shifted up or down | Normalization failure; majority-DE experiment may violate assumptions |

| Funnel shape widening at low expression | Expected — low-count genes have noisier fold changes |

| Discrete horizontal bands | Low-count artifacts; consider stronger pre-filtering |

Volcano Plot: Shrunken LFCs

Use shrunken LFCs (apeglm/ashr) on the x-axis and un-shrunken p-values on the y-axis. This combination gives stable fold change estimates while preserving the original significance assessment. Without shrinkage, low-count genes with extreme but unreliable fold changes dominate the plot edges.

Dispersion Plot Diagnostics

| Pattern | Meaning |

|---------|---------|

| Gene-wise points scattered around fitted line | Good model fit |

| Gene-wise points far above fitted line | Possible outlier genes or unmodeled batch effects |

| Fitted line flat (no trend) | Unusual — check if data is over-filtered or has unusual structure |

| Final estimates much lower than gene-wise | Expected — shrinkage toward the fitted trend |

PCA Diagnostics

| Pattern | Meaning | Action |

|---------|---------|--------|

| Clear separation by condition on PC1/PC2 | Strong biological signal | Proceed |

| Separation by batch, not condition | Batch effect dominates | Include batch in model; do NOT use corrected counts for DE |

| One sample far from its group | Potential outlier or sample swap | Check library QC metrics; consider removing |

| No separation on PC1/PC2 but present on PC3+ | Subtle effects | May still find DE genes; check dispersion estimates |

deseq2-basics - Generate DESeq2 results for visualization
edger-basics - Generate edgeR results for visualization
de-results - Filter genes before visualization
data-visualization/volcano-and-ma-plots - Custom ggplot2/matplotlib volcano + MA with LFC shrinkage
data-visualization/dimensionality-reduction-plots - PCA / UMAP / t-SNE / PHATE
data-visualization/heatmaps-clustering - Advanced heatmap customization

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How to use it

Copy the folder

Take biotender-max/bio-de-visualization from the repository into ~/.claude/skills for personal use, or into .claude/skills inside a project.

Check the name does not clash

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Bio De Visualization Agent Skill

Install

What comes with it

The instruction itself

Version Compatibility

DE Visualization

Scope

Required Libraries

Installation

MA Plot

DESeq2 MA Plot

Custom ggplot2 MA Plot

edgeR MA Plot

Volcano Plot

Basic Volcano Plot

Volcano with Gene Labels

EnhancedVolcano

PCA Plot

DESeq2 PCA

Custom PCA with ggplot2

edgeR PCA (via limma)

Heatmaps

Top DE Genes Heatmap

Sample Distance Heatmap

Gene Expression Heatmap

Dispersion Plot

DESeq2

edgeR

Counts Plot for Individual Genes

DESeq2

edgeR

P-value Histogram

Saving Plots

Color Palettes

Quick Reference: Common Plots

Diagnostic Interpretation

P-value Histogram

MA Plot Diagnostics

Volcano Plot: Shrunken LFCs

Dispersion Plot Diagnostics

PCA Diagnostics

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