MGKit: Metagenomic framework
0.3.4
  • Introduction
  • Installation
  • Metagenomic Pipeline
  • Scripts Details
  • Example Notebooks
    • Abundance Plots
    • Boxplots
    • Heatmaps
    • Misc. Plots Tips
    • Examples of the mgkit.db package
  • MGKit GFF Specifications
  • Library Reference
  • Changes
MGKit: Metagenomic framework
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  • Example Notebooks
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Example NotebooksΒΆ

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
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© Copyright 2013-2015, Francesco Rubino.

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