Input as knownResults folder Motif Visualization

[annrosebright]

Thank you for developing this fantastic tool for visualizing HOMER results! I truly appreciate your efforts in making data visualization more accessible.

I have a question about using the heatmap function: Can I use the knownResults.txt file as input? When I use the loadHomerRes function with the HOMER results directory, I notice that the number of motifs I can select is quite low (around 45) as it takes homerResults as directory and it has the low number of motifs. However, the knownResults.txt file and knownResults folder has many more motifs listed, which I also see in the associated HTML file.

I would like to display some specific motifs from the knownResults.txt file on the heatmap for a more complete view of my data. If you have any suggestions or guidance on how to do this, I would greatly appreciate it.

Thank you for your help!

[junjunlab]

Can you share your HOMER results, I will have a check.

[annrosebright]

summits.zip

Thank you for the response. Sharing the output folder with results in it. This was output of findMotifsGenome.pl.

[junjunlab]

I think you can set novo=F if you only want to perform known motifs analysis, here is the example code:

library(JunJunZai)

hr <- loadHomerRes(homerDir = "../summits/summits/",
                   novo = F,
                   motifIndex = 1:50)

hr

plotMotifHeatmap(object = hr,type = "known")

[annrosebright]

Thanks a lot. That worked.