MGKit: Metagenomic framework
0.4.1
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
Docs
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Example Notebooks
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Example Notebooks
ΒΆ
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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v: 0.4.1
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