This is the paper where they have first done co-expression analysis of TF and then found coexpressed modules which were further subjected to module clustering ,paper
So now im clear about the first part of doing the coexpression ,the part which they have written on the paper Im quoting
Using Pearson correlation coefficient of 0.4 as a cutoff to define a positive correlation between TF pairs, we obtained 37 tightly related TF modules that showed excellent co-expression patterns (Fig. 4a and Supplementary Data 4).We summed the average intensity of each module and then performed hierarchical clustering to reveal the relationship among the 37 TF modules
As of now If i have done something like this ,i use all the modules coming up with no threshold as such which they have written 0.4, if i get it, then the first figure is a gene-gene pair correlation, how to filter it ,because if i get try to set a threshold i will have to look for every pair irrespective of the module found ,
How to do it in R im not sure about it, any suggestion would be really helpful,next one is how are they going for the next one which is module clustering ,as there are 37 TF modules ,each of them having different gene distribution ,here the second figure the modules are in the rows if i understand ,so how have they done it i would like to get an idea about it.
Earlier i have asked a question , i have the data as if that can be used to show me how it can be done that would be really helpful.