Templates / PCA Plot
PCA Plot Template
Publication-quality PCA scatter plot with variance-explained axis labels, 95% confidence ellipses, and sample grouping. Standard for bulk RNA-seq, proteomics, and metabolomics quality control and exploratory analysis.
Use this template →Template specifications
Chart type
PCA scatter plot
X-axis
PC1 (X% variance)
Y-axis
PC2 (Y% variance)
Ellipses
95% confidence ellipses by group
Scaling
Center + scale (Z-score) by feature
Point shape
Varies by group (colorblind-safe)
Sample labels
Optional; ggrepel-style non-overlap
Aspect ratio
Equal (square)
Export
TIFF 300–1200 DPI / PDF
Input data format
Paste a samples × features matrix (normalized, log-transformed). FigureGuild runs PCA internally and calculates variance explained.
# expression_matrix.csv (samples as rows)
sample, Gene1, Gene2, Gene3, ...
Control_1, 5.2, 3.1, 8.4, ...
Control_2, 4.9, 3.4, 8.1, ...
Treatment_1, 7.1, 2.0, 6.3, ...
Full guide: How to create a PCA plot for scientific publication