Getting Started | Install chromoMap | Prepare Input Data Files | Chromosome Files | Annotation Files | chromoMap files for this vignette | R objects as chromoMap Inputs | My first chromoMap | Polyploidy | Point and Segment-annotation plots | High-Resolution Maps | Window Scaling | Fixed-Window | Data-based annotation plots | chromoMap-DiscreteColorMaps | Manually setting the order of categories | chromoMap-HeatMaps | Data Aggregation | Manually changing the data domain for heatmap | chromoMap-Bar Plots | chromoMap-Scatter Plots | epi-tags | chromoMap-Filters | tag-filters | plot-filters | multi-factor scatter plots | 2D-Chromosome Plots | 2D-Chr Heatmaps | for Numeric Data | for Categorical Data | chromLinks Plots | Visualizing links as Edges | color mapping links data | directed edges | Visualizing links as Chords | Customizing chromoMaps | width and height | Title | Margins | Chromosome colors | Annotation colors | Chromosome width, length, and spacing | Chromosome curves | Chromsome scale y-position | Chromosome text | Interactivity | Chr Scale Suffix | Chr Scale Ticks | Show/hide Chromosomes | Guides | plot ID | Automatic color assignments | Customizing Data Plots | Reference Lines | Plot height | Plot Colors | Plot y-axis range and ticks | Plot y Labels | Highlighting with grid lines | adding labels to grid lines | Quick Zoom-in | highlighting a region | zooming in on that region | Legends | positioning legends | Legend labels | Labellings | Hyperlinks | Export to PNG/SVG/HTML | In-built Export Options | Including chromoMaps in Shiny Applications | Shiny Application example | license | Contact | Cite | Session Info