Boxplot API

Boxplot FUNCTION

This API provides a function to create a customizable boxplot from KEGGaNOG multi mode output, typically used to visualize pathway completeness across multiple samples.

It includes features for styling axes, grid lines, background color, and boxplot outlier visibility.

boxplot(df, ...)

PARAMETERS

PARAMETER	DESCRIPTION
df	Input data as a pandas DataFrame TYPE: pd.DataFrame
figsize	Size of the figure (width, height) TYPE: Tuple[int, int] DEFAULT: (12, 6)
color	Box color TYPE: str or None DEFAULT: "blue"
showfliers	Whether to show outlier points TYPE: bool DEFAULT: True
title	Plot title TYPE: str or None DEFAULT: None
title_fontsize	Font size of title TYPE: float DEFAULT: 16.0
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"
xlabel	Label for X-axis TYPE: str DEFAULT: "Samples"
xlabel_fontsize	Font size of X-axis label TYPE: float DEFAULT: 14.0
xlabel_color	Font color of X-axis label TYPE: str DEFAULT: "black"
xlabel_weight	Font weight of X-axis label TYPE: str DEFAULT: "normal"
xlabel_style	Font style of X-axis label TYPE: str DEFAULT: "normal"
ylabel	Label for Y-axis TYPE: str DEFAULT: "Completeness Value"
ylabel_fontsize	Font size of Y-axis label TYPE: float DEFAULT: 14.0
ylabel_color	Font color of Y-axis label TYPE: str DEFAULT: "black"
ylabel_weight	Font weight of Y-axis label TYPE: str DEFAULT: "normal"
ylabel_style	Font style of Y-axis label TYPE: str DEFAULT: "normal"
xticks_rotation	Rotation angle for X-axis tick labels TYPE: float DEFAULT: 45.0
xticks_ha	Horizontal alignment of X-axis ticks TYPE: str DEFAULT: "center"
xticks_fontsize	Font size of X-axis ticks TYPE: float DEFAULT: 12.0
xticks_color	Font color of X-axis ticks TYPE: str DEFAULT: "black"
xticks_weight	Font weight of X-axis ticks TYPE: str DEFAULT: "normal"
xticks_style	Font style of X-axis ticks TYPE: str DEFAULT: "normal"
yticks_fontsize	Font size of Y-axis ticks TYPE: float DEFAULT: 12.0
yticks_color	Font color of Y-axis ticks TYPE: str DEFAULT: "black"
yticks_weight	Font weight of Y-axis ticks TYPE: str DEFAULT: "normal"
yticks_style	Font style of Y-axis ticks TYPE: str DEFAULT: "normal"
grid	Display grid TYPE: bool DEFAULT: True
grid_color	Color of grid lines TYPE: str DEFAULT: "grey"
grid_linestyle	Style of grid lines TYPE: str DEFAULT: "--"
grid_linewidth	Width of grid lines TYPE: float DEFAULT: 0.5
background_color	Background color of the figure TYPE: str or None DEFAULT: None

RETURNS

Returns an object with:

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

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

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 easily build a boxplot on KEGGaNOG output

import kegganog as kgn
import pandas as pd

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

kgnbox = kgn.boxplot(
    df,
    color="#90ee90",
    title="", title_fontsize = 12, title_weight = "normal",
    xticks_rotation = 0,
    ylabel="Pathways completeness value", ylabel_fontsize = 12, ylabel_weight = "normal",
    figsize=(10, 6),
)

# To plot a fig please use:
kgnbox.plotfig()

Sample output:

kgn.boxplot() returns an object containing the boxplot figure and axis, so, user is able to further customize its plot!
E.g. the user wants to visually highlight a completeness threshold of 0.3 across samples:

kgnbox.ax.axhline(0.3, color="red", linestyle="--", linewidth=1.5)

kgnbox.plotfig()

Sample output:

For saving a plot please use:

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