Documents of Oviz-Bio, a Platform for Bioinformatics Visualization

The LandScape visualization is frequently utilized to provide a systematic illustration of integrative data from multiple layers of batch samples, which are always compared to each other on certain attributes, such as genes and biological pathways mutated in cancers. To visualize data, a CSV file in the required format is needed.

• Check the official demo input here.
• PMID prefixed CSV files to present LandScape instances of published papers (see Reference).

The Mutations on Genes displays SNVs and InDels with their coordinates and function annotations along the selected transcript of a given gene in three levels (genome, cDNA, and peptide).

• Check the official demo input here.

The SNV: Context visualization, otherwise known as the Lego plot of mutational frequencies, describes the distribution of mutations across batch samples on a given region.

• Check the official demo input here.

The SNV: Signature visualization is wildly used in mutational signature analysis. It shows the signature profile with the conventional 96 mutation type classification. We also compare each signature with all recorded signature references in the COSMIC database by the cosine similarity test. The top three similar signature references are listed with their percentage of similarity.

• Check the official demo input here.

The Mut: Signature Dist visualization shows the fraction of signatures within individual samples. It can also be used to show the fraction of signatures within several cancer types.

• Check the official demo input here.

The CNV: Haplotype View visualization is an interactive version of the output plot from Patchwork, a bioinformatics tool for analyzing allele-specific copy numbers and loss-of-heterozygosity in cancer genomes. This visualization summarizes all 24 chromosomal plots generated by Patchwork and provides user with the choice to highlight information of one particular chromosome.

• Check the official demo input here.
• User can directly use the output from the Patchwork tool as our input file.

The CNV: Focal Cluster visualization is an interactive and extended version of the output plot from GISTIC, a bioinformatics tool for identifying regions of the genome that are significantly amplified or deleted across a set of samples.

• Check the official demo input here.
• User can directly use the output from the GISTIC tool as our input file.

The SV: Reads Support visualization is frequently utilized to provide the detail illustration of supporting split reads for given SV events. To visualize data, a TXT file in the required format is needed.

• Check the official demo input here.

Linkage heatmap is an useful method to visualize read linkage patterns on SV event, especially in studies with long-range sequencing data, such as 10x linked-reads. We apply the SV: Heatmap visualization to display the heatmap matrix based on sequencing reads linkage between two local windowlized regions of SV case. The color depth of each cross-linked window pair is proportional to the number of linkages. Along the chromosome coordinate axis of the heatmap matrix, annotation information is added, such as Ensembl genes. To visualize data, upload a TXT file in the required format, and then use sidebar options to adjust heatmap color scheme and choose other SVs to display if uploaded data contains multiple cases.

• Check the official demo input here.

the Fusion: Trans Junction visualization displays the whole structure of chimeric transcript structure.

• Check the official demo input here.

the Virus: Integ HotSpot visualization displays the oncovirus integrated hotspot of group samples in a genome browser way.

• Check the official demo input here.
• HBV_PMID22634754.csv and HPV_PMID25581428.csv record integration cases of oncovirus HBV and HPV, respectively.