python条形图16S细菌丰度

Question

我有这种数据（data.txt），制表符分隔文本中的文件）：

#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，一个像图片（从其他页面取得的一个例子）bar chart plot

在这种情况下，我有两个样本（data1和data2），但可能很多，可能是数百或数千个分类单元（属）并且难以逐个选择颜色，因此每个分类单元的颜色必须被自动分配。任何人都有一个python脚本，加载这种格式的txt文件并绘制它？

很抱歉，如果我没有输入任何代码，我不知道如何在python中编码，我已尝试使用QIIME，但我必须删除大量文本（例如：D_0__Bacteria; D_1__Beteroidetes; D_2__Flavobacteriia; D_3__Flavobacteriales; D_4__Cryomorphaceae; D_5__Fluviicola）所以我制作了一个perl脚本来提取刚属（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 https://stackoverflow.com/q/39839409/50065
# choose an appropriate pallete from
# https://bokeh.pydata.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
# https://stackoverflow.com/questions/48240867/how-can-i-make-legend-outside-plot-area-with-stacked-bar
new_legend = p.legend[0]
p.legend[0].plot = None
p.add_layout(new_legend, 'right')

show(p)

这会创建：