Stacked Barplot API

Stacked Barplot FUNCTION

This API provides a function to create a stacked bar plot from KrakenParser relative abundance tables.

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PARAMETERS

PARAMETER	DESCRIPTION
df	Input data as a pandas DataFrame TYPE: pd.DataFrame
metadata	Optional DataFrame with sample metadata (must include 'Sample_id') TYPE: pd.DataFrame
metadata_group	Column in metadata to group samples by for aggregation TYPE: str
sample_order	The order of columns (samples) TYPE: list
figsize	Size of the figure (width, height) TYPE: Tuple[int, int] DEFAULT: (14, 7)
cmap	Colormap name (e.g. "tab20") or list of HEX colors for pathway groups TYPE: str or List[str] DEFAULT: "tab20"
bar_width	Width parameter for bars TYPE: float DEFAULT: 0.6
edgecolor	Color of the edges around each stacked area TYPE: str DEFAULT: "black"
edge_linewidth	Line width of group borders in each stacked bar TYPE: float DEFAULT: 0.3
title	Plot title TYPE: str or None DEFAULT: None
title_fontsize	Font size of the title TYPE: float DEFAULT: 16.0
title_color	Font color of the title TYPE: str DEFAULT: "black"
title_weight	Font weight of the title TYPE: str DEFAULT: "normal"
title_style	Font style of the title TYPE: str DEFAULT: "normal"
xlabel	Label for the x-axis TYPE: str DEFAULT: "Samples"
xlabel_fontsize	Font size for x-axis label TYPE: float DEFAULT: 12.0
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 the y-axis TYPE: str DEFAULT: "Total Completeness"
ylabel_fontsize	Font size for y-axis label TYPE: float DEFAULT: 12.0
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 of x-axis tick labels TYPE: float DEFAULT: 45.0
xticks_ha	Horizontal alignment of x-axis tick labels TYPE: str DEFAULT: "center"
xticks_fontsize	Font size of x-axis tick labels TYPE: float DEFAULT: 12.0
xticks_color	Font color of x-axis tick labels TYPE: str DEFAULT: "black"
xticks_weight	Font weight of x-axis tick labels TYPE: str DEFAULT: "normal"
xticks_style	Font style of x-axis tick labels TYPE: str DEFAULT: "normal"
grid	Whether to show grid lines TYPE: bool DEFAULT: True
grid_linestyle	Line style for the grid (e.g. "--") TYPE: str DEFAULT: "--"
grid_alpha	Transparency of grid lines TYPE: float DEFAULT: 0.7
legend_fontsize	Font size of the legend TYPE: float DEFAULT: 9.0
legend_fontstyle	Font style of the legend TYPE: str DEFAULT: "italic"
legend_loc	Location of the legend TYPE: str DEFAULT: "upper left"
legend_bbox	Manual anchor for legend box TYPE: Tuple[float, float] DEFAULT: (1.05, 1)
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
• ax: the Matplotlib axis

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

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USAGE EXAMPLE

Where to get demo data? Here

import krakenparser as kp
import pandas as pd

df = pd.read_csv("demo_data/counts/csv_relabund/counts_species_2.csv")

kpstbar = kp.stacked_barplot(
    df,
    figsize=(12, 6),
    bar_width = 0.6,
    edge_linewidth = 0.6,
    cmap="tab20",
    xticks_fontsize=12,
    background_color=None
    )

# Show the figure
kpstbar.plotfig()

Sample output:

To save the plot:

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