使用deepTools里的命令时出现错误：
Traceback (most recent call last):
File "/usr/local/bin/plotCorrelation", line 5, in <module>
from deeptools.plotCorrelation import main
File "/usr/local/lib/python2.7/dist-packages/deeptools/plotCorrelation.py", line 6, in <module>
import numpy as np
ImportError: No module named numpy就是说没有numpy这个模块，我们需要安装它。
输入pip install numpy，出现以下错误：
Requirement already satisfied: numpy in /usr/local/lib/python3.8/dist-packages (1.22.3)这是因为numpy被安装到了/usr/local/lib/python3.8/dist-packages (1.22.3)目录下，而我们的python则在另外一个目录中。查看python目录
输入：whereis python
python: /usr/bin/python /usr/bin/python2.7 /usr/bin/python2.7-config /usr/bin/python3.8
/usr/bin/python3.8-config /usr/lib/python2.7 /usr/lib/python3.8 /usr/lib/python3.9
/etc/python2.7 /etc/python3.8 /usr/local/lib/python2.7 /usr/local/lib/python3.8
/usr/include/python2.7 /usr/include/python3.8 /usr/share/python把numpy安装到正确的python目录中。
输入su root，开启管理员权限，然后输入：
pip install --target=<目录> numpy
<目录>就是python的安装目录下的dist-packages，比如我就输入
pip install --target=/usr/local/lib/python3.8/dist-packages numpy
再用deeptools的工具测试，输入：plotCorrelation，差哪个就pip install哪个，直到所有install完成
直到显示
usage: plotCorrelation [-h] --corData FILE --corMethod {spearman,pearson} --whatToPlot {heatmap,scatterplot}
[--plotFile FILE] [--skipZeros] [--labels sample1 sample2 [sample1 sample2 ...]]
[--plotTitle PLOTTITLE] [--plotFileFormat FILETYPE] [--removeOutliers] [--version]
[--outFileCorMatrix FILE] [--plotHeight PLOTHEIGHT] [--plotWidth PLOTWIDTH] [--zMin ZMIN]
[--zMax ZMAX] [--colorMap] [--plotNumbers] [--xRange XRANGE XRANGE] [--yRange YRANGE YRANGE]
[--log1p]
Tool for the analysis and visualization of sample correlations based on the output of multiBamSummary or
multiBigwigSummary. Pearson or Spearman methods are available to compute correlation
coefficients. Results can be saved as multiple
scatter plots depicting the pairwise correlations or as a clustered heatmap,
where the colors represent the correlation coefficients and the clusters are constructed using complete linkage.
Optionally, the values can be saved as tables, too.
detailed help:
plotCorrelation -h
optional arguments:
-h, --help show this help message and exit
Required arguments:
--corData FILE, -in FILE
Compressed matrix of values generated by multiBigwigSummary or multiBamSummary
--corMethod {spearman,pearson}, -c {spearman,pearson}
Correlation method.
--whatToPlot {heatmap,scatterplot}, -p {heatmap,scatterplot}
Choose between a heatmap or pairwise scatter plots
Optional arguments:
--plotFile FILE, -o FILE
File to save the heatmap to. The file extension determines the format, so heatmap.pdf will
save the heatmap in PDF format. The available formats are: .png, .eps, .pdf and .svg.
--skipZeros By setting this option, genomic regions that have zero or missing (nan) values in all samples
are excluded.
--labels sample1 sample2 [sample1 sample2 ...], -l sample1 sample2 [sample1 sample2 ...]
User defined labels instead of default labels from file names. Multiple labels have to be
separated by spaces, e.g. --labels sample1 sample2 sample3
--plotTitle PLOTTITLE, -T PLOTTITLE
Title of the plot, to be printed on top of the generated image. Leave blank for no title.
(Default: )
--plotFileFormat FILETYPE
Image format type. If given, this option overrides the image format based on the plotFile
ending. The available options are: png, eps, pdf and svg.
--removeOutliers If set, bins with very large counts are removed. Bins with abnormally high reads counts
artificially increase pearson correlation; that's why, multiBamSummary tries to remove
outliers using the median absolute deviation (MAD) method applying a threshold of 200 to only
consider extremely large deviations from the median. The ENCODE blacklist page
(https://sites.google.com/site/anshulkundaje/projects/blacklists) contains useful information
about regions with unusually high countsthat may be worth removing.
--version show program's version number and exit
Output optional options:
--outFileCorMatrix FILE
Save matrix with pairwise correlation values to a tab-separated file.
Heatmap options:
--plotHeight PLOTHEIGHT
Plot height in cm. (Default: 9.5)
--plotWidth PLOTWIDTH
Plot width in cm. The minimum value is 1 cm. (Default: 11)
--zMin ZMIN, -min ZMIN
Minimum value for the heatmap intensities. If not specified, the value is set automatically
--zMax ZMAX, -max ZMAX
Maximum value for the heatmap intensities.If not specified, the value is set automatically
--colorMap Color map to use for the heatmap. Available values can be seen here:
http://matplotlib.org/examples/color/colormaps_reference.html
--plotNumbers If set, then the correlation number is plotted on top of the heatmap. This option is only
valid when plotting a heatmap.
Scatter plot options:
--xRange XRANGE XRANGE
The X axis range. The default scales these such that the full range of dots is displayed.
--yRange YRANGE YRANGE
The Y axis range. The default scales these such that the full range of dots is displayed.
--log1p Plot the natural log of the scatter plot after adding 1. Note that this is ONLY for plotting,
the correlation is unaffected.
example usages:
plotCorrelation -in results_file --whatToPlot heatmap --corMethod pearson -o heatmap.png代表可以使用了。
su <你的用户名>就可以回到自己的账户。
