Matlab:具有统一绘图列高度的 seqlogo
在Matlab中,我想制作一个seqlogo图氨基酸序列概况。但我不希望通过熵来缩放绘图列的高度,而是希望所有列具有相同的高度。
我正在修改 答案中的代码这个问题,但我想知道是否有 seqlogo 的参数或我错过的其他一些函数可以使列高度统一。
或者,是否可以对序列配置文件应用统计转换来破解所需的输出? (列高统一,每个字母的高度与 它在 seqprofile 中的概率)
In Matlab, I want to make a seqlogo plot of an amino acid sequence profile. But instead of scaling the heights of the plot columns by entropy, I want all the columns to be the same height.
I'm in the process of modifying the code from the answers to this question, but I wonder if there is a parameter to seqlogo or some other function that I have missed that will make the column heights uniform.
Alternatively, is there a statistical transformation I can apply to the sequence profile to hack the desired output? (column heights uniform, height of each letter linearly proportion to
its probability in the seqprofile)
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解决此问题的最简单方法可能是直接修改 生物信息学的代码工具箱函数 SEQLOGO(如果可能)。在 R2010b 中,您可以执行以下操作:
该函数的代码将显示在编辑器中。接下来,找到以下行(第 267-284 行),然后将其注释掉或完全删除:
然后将此行放在其位置:
您可能希望以新名称保存文件,例如 seqlogo_norm.m ,因此您仍然可以使用原始未修改的SEQLOGO 函数。现在,您可以创建序列剖面图,其中所有列均标准化为相同高度。例如:
旧答案:
我不是确定如何转换序列配置文件信息以从 生物信息学获得所需的输出工具箱函数 SEQLOGO,但我可以向您展示如何修改我为 我对您链接到的相关问题的回答。如果将初始化
bitValues
的行从以下位置更改为:
则应将每列的高度缩放为 1。例如:
Probably the easiest way around this problem is to directly modify the code for the Bioinformatics Toolbox function SEQLOGO (if possible). In R2010b, you can do:
And the code for the function will be shown in the editor. Next, find the following lines (lines 267-284) and either comment them out or remove them entirely:
Then put this line in their place:
You will probably want to save the file under a new name, like
seqlogo_norm.m
, so you can still use the original unmodified SEQLOGO function. Now you can create sequence profile plots with all the columns normalized to the same height. For example:OLD ANSWER:
I'm not sure how to transform the sequence profile information to get the desired output from the Bioinformatics Toolbox function SEQLOGO, but I can show you how to modify the alternative
seqlogo_new.m
that I wrote for my answer to the related question you linked to. If you change the line that initializesbitValues
from this:to this:
Then you should get each column scaled to a height of 1. For example:
目前,我的解决方法是生成一堆与序列配置文件匹配的假序列,然后将这些序列提供给 http ://weblogo.berkeley.edu/logo.cgi。这是制作假序列的代码:
For now, my workaround is to generate a bunch of fake sequences that match the sequence profile, then feed those sequences to http://weblogo.berkeley.edu/logo.cgi . Here is the code to make the fake sequences: