Barplot API

Barplot FUNCTION

This API provides a function to create a customizable horizontal barplot from KEGGaNOG single mode output, typically used to visualize pathways completeness — it only takes pathways with completeness > 0.

barplot(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: (8, 12)
cmap	Colormap name or list of colors TYPE: str or list DEFAULT: "Greens"
cmap_range	Colormap index range TYPE: Tuple[int, int] DEFAULT: (8, 30)
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: "Pathway completeness"
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: "Pathway"
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_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_linestyle	Line style of grid lines TYPE: str DEFAULT: "--"
grid_alpha	Opacity of grid lines TYPE: float DEFAULT: 0.5
background_color	Background color of the figure TYPE: str or None DEFAULT: None
sort_order	Sort bars by value ("ascending" or "descending") 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 single-sample mode

Where to get demo data? Here

! KEGGaNOG -i demo_data/LaPla/LaPla.emapper.annotations -o KEGGaNOG_single_output

Then user can easily build a barplot on KEGGaNOG output

import kegganog as kgn
import pandas as pd

df = pd.read_csv("KEGGaNOG_single_output/SAMPLE_pathways.tsv", sep="\t")

kgnbar = kgn.barplot(df,
    figsize = (8, 10),
    sort_order="descending",
    yticks_fontsize = 8, 
    cmap = "Blues",
)

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

Sample output:

kgn.barplot() returns an object containing the barplot figure and axis, so, user is able to further customize its plot!
E.g. user wants to divide pathways with completeness > 0.5 and < 0.5:

kgnbar.ax.axvline(0.5, color="red", linestyle="--")

kgnbar.plotfig()

Sample output:

For saving a plot please use:

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