Example Notebooks

Example notebooks are included about using the library

• Abundance Plots
  • Triangle Plot
    • Grid
    • Plot
  • Abundance Plot with 2 Samples
    • Grid
• Boxplots
  • Simple boxplot
  • Change order of boxplots
  • Change labels
  • Change font parameters
  • Empty boxplots
  • Vertical boxplot
  • Change boxplot colors
  • Change data colors and the median color
  • Adding data points
  • Adding Significance annotations
    • Changed direction, different palette and marker
• Heatmaps
  • Random matrix and color map init
  • Basic plot
  • Add numbers to the heatmap
    • Default
    • Change format of numbers
  • Using Boundaries for the colors
  • Normalising the colors
    • Grouping labels
    • Reversing the order of the rows
  • A dendrogram from clustering the data
    • Clustering rows
    • Clustering colums (You need the transposed matrix)
  • A simple clustered heatmap, look at the code for customisation
• Misc. Plots Tips
  • Trim Figure
• Examples of the mgkit.db package
  • Imports
  • Download Example GFF
  • GFF Annotations
    • Taxonomy and Annotations
    • Issues
  • semidbm
  • Using MongoDB
    • Using Taxonomy