在Python和Rpy2中使用R:如何进行ggplot2? [英] Using R in Python with Rpy2: how to ggplot2?
问题描述
大家好,我试图在Python中使用R,但我发现Rpy2非常有趣.它功能强大并且使用起来并不难,但是即使我已经阅读了文档并寻找了类似的问题,我也无法使用ggplot2库解决我的问题.
Hi guys I'm trying to use R in Python and I found Rpy2 very interesting. It is powerful and not that difficult to use, however even if I have read the documentation and looked for a similar question, I wasn't able to solve my problem with the ggplot2 library.
基本上,我有一个包含2列,11行且没有标题的数据集,我想使用Python中的以下R代码绘制散点图:
Basically I have a dataset with 2 columns, 11 rows and no header and I would like to do a scatter plot using this R code from Python:
ggplot(dataset,aes(dataset$V1, dataset$V2))+geom_point()+scale_color_gradient(low="yellow",high="red")+geom_smooth(method='auto')+labs(title = "Features distribution on Scaffolds", x='Scaffolds Length', y='Number of Features')
我已经在R中测试了此代码(在文件的read.table之后),它可以工作.现在,这是我的python脚本:
I have tested this code in R (after read.table my file) and it works. Now, this is my python script:
import math, datetime
import rpy2
import rpy2.robjects as robjects
import rpy2.robjects.lib.ggplot2 as ggplot2
r = robjects.r
df = r("read.table('file_name.txt',sep='\t', header=F)")
gp = ggplot2.ggplot(df, ggplot2.aes(df[0], df[1])) + ggplot2.geom_point() + ggplot2.scale_color_gradient(low="yellow",high="red") + ggplot2.geom_smooth(method='auto') + ggplot2.labs(title = "Features distribution on Scaffolds", x='Scaffolds Length', y='Number of Features')
gp.plot()
如果我运行此Python代码,它将给我两个错误.第一个是:
If i run this Python code, it gives me two errors. The first is:
gp = ggplot2.ggplot(df, ggplot2.aes(df[0], df[1]))
TypeError: new() takes exactly 1 argument (3 given)
第二个是:
AttributeError: 'module' object has no attribute 'scale_color_gradient'
有人可以帮我了解我错了吗?
Can someone help me to understand where I'm wrong please?
非常感谢您的光临!
马西米利亚诺(Massimiliano).
Massimiliano.
推荐答案
也许您需要将数据框列与散点图的颜色相关联
点,以便scale_colour_gradient
可以与该列关联:
Perhaps you need to associate a dataframe column to the colour of the scatter
points so that the scale_colour_gradient
can be associated to that column:
import numpy as np
import pandas as pd
import rpy2.robjects.packages as packages
import rpy2.robjects.lib.ggplot2 as ggplot2
import rpy2.robjects as ro
R = ro.r
datasets = packages.importr('datasets')
mtcars = packages.data(datasets).fetch('mtcars')['mtcars']
gp = ggplot2.ggplot(mtcars)
pp = (gp
+ ggplot2.aes_string(x='wt', y='mpg')
+ ggplot2.geom_point(ggplot2.aes_string(colour='qsec'))
+ ggplot2.scale_colour_gradient(low="yellow", high="red")
+ ggplot2.geom_smooth(method='auto')
+ ggplot2.labs(title="mtcars", x='wt', y='mpg'))
pp.plot()
R("dev.copy(png,'/tmp/out.png')")
错误
gp = ggplot2.ggplot(df, ggplot2.aes(df[0], df[1]))
TypeError: new() takes exactly 1 argument (3 given)
出现
的原因是ggplot2.ggplot
仅接受1个参数,即数据帧:
occurred because ggplot2.ggplot
takes only 1 argument, the dataframe:
gp = ggplot2.ggplot(df)
然后可以将美学映射添加到gp
:
You can then add the aesthetics mapping to gp
:
gp + ggplot2.aes_string(x='0', y='1')
,其中'0'
和'1'
是df
的列名.根据文档中示例,我在这里使用的是aes_string
而不是aes
.
where '0'
and '1'
are column names of df
. Per the examples in the docs, I've used aes_string
here instead of aes
.
第二个错误
AttributeError: 'module' object has no attribute 'scale_color_gradient'
发生是因为ggplot2使用英国的颜色拼写:scale_colour_gradient
:
occurred because ggplot2 uses the British spelling of color: scale_colour_gradient
:
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