🧬 PseudoScope Comprehensive Dashboard
Interactive visualisation of Pseudomonas aeruginosa genomic data – ST and O‑type distributions, resistance/virulence gene prevalence, co‑occurrence networks, assembly quality, and multivariate analysis.
📊 MLST & Serotype Distribution
ST and O‑type prevalence – Bars show the number of genomes per Sequence Type (Pasteur scheme) and O‑serotype. Hover for exact counts.
💊 Top AMR & Virulence Genes
Stacked bar charts – Each bar represents a gene; segments show contributions from different databases (AMRfinder, NCBI, CARD, ResFinder, etc.). Only the top 50 most prevalent genes are shown (adjustable in script).
🔗 Gene Co‑occurrence Network
Network of gene co‑occurrence – Nodes are genes; edges connect genes that appear together in at least one genome. Edge count is based on the top 100 co‑occurrence pairs. Node size reflects degree (number of connections). Hover for details.
📈 FASTA Assembly Quality
QC metrics distribution – Each box plot shows the spread of GC%, AT%, N50 (contiguity), and total assembly length. All individual data points are shown as dots (jittered). N50 and Total Length are on a log scale.
📐 Principal Component Analysis (PCA)
Gene presence/absence PCA – Each point is a genome, colored by ST. The plot reduces the high‑dimensional gene profile to two principal components. Clusters indicate similar resistance/virulence gene complements.
🔥 AMR Gene Co‑occurrence Heatmap
Pairwise co‑occurrence counts – Darker red indicates that two AMR genes appear together more often. Helps identify linked resistance determinants. Shown for top 30 AMR genes.