Radarplot API

Radarplot FUNCTION

This API provides a function to create a radar plot from KEGGaNOG multi-sample output. It visualizes completeness values of selected pathways across multiple samples in a circular (radial) format.

radarplot(df, pathways, ...)

PARAMETERS

PARAMETER	DESCRIPTION
df	Input data as a pandas DataFrame TYPE: pd.DataFrame
pathways	List of pathway names to include in the radar plot TYPE: List[str]
figsize	Size of the figure (width, height) TYPE: Tuple[int, int] DEFAULT: (8, 8)
colors	List of colors for the samples TYPE: List[str] or None DEFAULT: None
sample_order	Custom order of sample names TYPE: List[str] or None DEFAULT: None
title	Plot title TYPE: str or None DEFAULT: None
title_fontsize	Font size of title TYPE: float DEFAULT: 14.0
title_color	Font color of title TYPE: str DEFAULT: "black"
title_weight	Font weight of title TYPE: str DEFAULT: "normal"
title_style	Font style of title TYPE: str DEFAULT: "normal"
title_y	Vertical alignment of the title TYPE: float DEFAULT: 1.1
label_fontsize	Font size of axis labels (pathways) TYPE: float DEFAULT: 10.0
label_color	Font color of axis labels TYPE: str DEFAULT: "black"
label_weight	Font weight of axis labels TYPE: str DEFAULT: "normal"
label_style	Font style of axis labels TYPE: str DEFAULT: "normal"
label_background	Background color of axis labels TYPE: str or None DEFAULT: None
label_edgecolor	Edge color of axis label boxes TYPE: str or None DEFAULT: None
label_pad	Padding for labels TYPE: float DEFAULT: 1.05
ytick_fontsize	Font size of radial axis ticks TYPE: float DEFAULT: 8.0
ytick_color	Font color of radial axis ticks TYPE: str DEFAULT: "black"
ytick_weight	Font weight of radial axis ticks TYPE: str DEFAULT: "normal"
ytick_alpha	Alpha (opacity) of radial ticks TYPE: float DEFAULT: 0.5
yticklabels	Custom labels for radial axis ticks TYPE: List[str] or None DEFAULT: None
fill_alpha	Transparency of the filled area TYPE: float DEFAULT: 0.2
line_width	Line width of radar plot borders TYPE: float DEFAULT: 2.0
line_style	Line style TYPE: str DEFAULT: "-"
legend_loc	Legend position keyword TYPE: str DEFAULT: "upper right"
legend_bbox	Manual legend box anchor TYPE: Tuple[float, float] or None DEFAULT: None
show_legend	Whether to display legend TYPE: bool DEFAULT: True
background_color	Background color of the figure TYPE: str or None DEFAULT: None

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RETURNS

Returns an object with:

• fig: the Matplotlib figure object
• ax: the Matplotlib axis object

The object includes .plotfig() and .savefig() methods for convenience.

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USAGE EXAMPLE

First, run KEGGaNOG in multi-sample mode:

Where to get demo data? Here

! KEGGaNOG -M -i demo_data/listFile.txt -o KEGGaNOG_multi_output

Then you can build a radar plot of selected pathways across samples:

import kegganog as kgn
import pandas as pd

df = pd.read_csv("KEGGaNOG_multi_output/merged_pathways.tsv", sep="\t")

# List of pathways to visualize
pathways = ["Glycolysis", "Chemotaxis", "Cobalamin biosynthesis"]
# Order of samples on radar plot
sample_order = ["SoCe", "PsePu", "CloAce", "BaSu", "MeRu", "AciSa", "StaCa", "LaPla", "BaThe", "TheMa"]


kgnradar = kgn.radarplot(
    df,
    pathways=pathways,
    sample_order=sample_order,
    label_weight="bold",
    label_background="white",
    label_edgecolor="black",
    label_pad=1.15,
    colors=["#1f77b4", "#2ca02c", "#ff7f0e"],
    yticklabels=["0.2", "", "0.6", "", "1.0"],
    fill_alpha=0.15
)

# Show the figure
kgnradar.plotfig()

Sample output:

To save the plot:

kgnradar.savefig("pic_name.png", dpi=600)