python 16S 细菌丰度条形图

Question

我有这种数据（data.txt），一个制表符分隔文本文件）：

#genera        data1    data2
Crocinitomix    0.000103252 0
Fluviicola      2.58E-05    0
uncultured      0.000180692 0.000103252
Actibacter      2.58E-05    0
Aquibacter      0.0003  0.002503872
Litoribaculum   0.000516262 0.1
Lutibacter      2.58E-05    0
Lutimonas       5.16E-05    0.00001
Ulvibacter      0   0
uncultured      0.00240062  0
Bacteroidetes bacterium 5.16E-05    2.58E-05
bacterium       0.000129066 0

我想创建一个条形图，如图所示（从其他页面获取的示例）bar chart plot

在这种情况下，我有两个样本（data1和data2），但可能很多，可能是成百上千个类群（属），很难一一选择颜色，所以每个颜色taxa 必须自动分配。任何人都有 python 脚本，可以加载这种格式的 txt 文件并绘制它？

对不起，如果我不放任何代码，我不知道如何在python中编码，我试过QIIME，但我必须删除很多文本（例如：D_0__Bacteria;D_1__Bacteroidetes;D_2__Flavobacteriia;D_3__Flavobacteriales;D_4__Cryomorphaceae;D_5__Fluviicola) 所以我制作了一个 perl 脚本来提取属 (D_5__), 现在，我只需要绘制它 !!!

非常感谢！！！

Answer 1

有很多方法可以解决这个问题，这里是使用pandas和bokeh的解决方案：

import pandas as pd
from bokeh.io import show, output_file
from bokeh.models import ColumnDataSource
from bokeh.plotting import figure
from bokeh.core.properties import value
from bokeh.palettes import Spectral
import itertools  

output_file("stacked.html")

df = pd.read_csv('bacteria.txt', sep='\t')
df.set_index('#genera', inplace=True)

samples = df.columns.values
organisms = df.index.values

# You have two rows with 'uncultured' data. I added these together.
# This may or may not be what you want.
df = df.groupby('#genera')[samples].transform('sum')

# create a color iterator
# See 
# choose an appropriate pallete from
# https://docs.bokeh.org/en/latest/docs/reference/palettes.html
# if you have a large number of organisms
color_iter = itertools.cycle(Spectral[11])    
colors = [next(color_iter) for organism in organisms]

# create a ColumnDataSource
data = {'samples': list(samples)}
for organism in organisms:
    data[organism] = list(df.loc[organism])
source = ColumnDataSource(data=data)

# create our plot
p = figure(x_range=samples, plot_height=250, title="Species abundance",
           toolbar_location=None, tools="")

p.vbar_stack(organisms, x='samples', width=0.9, source=source,
             legend=[value(x) for x in organisms], color=colors)

p.xaxis.axis_label = 'Sample'
p.yaxis.axis_label = 'Value'
p.legend.location = "top_right"
p.legend.orientation = "vertical"

# Position the legend outside the plot area
# 
new_legend = p.legend[0]
p.legend[0].plot = None
p.add_layout(new_legend, 'right')

show(p)

这将创建：

python 16S 细菌丰度条形图

python bar chart plot of 16S bacterial abundance

python

bioinformatics

bar-chart

biopython