I have a file that has enhancers in 1st column and the name of transcription factor in 2nd column for which it has binding sites. I want to see this data visually so I can know which enhancers share similar transcription factor binding sites. How can I make a heatmap out of it? or any other visual graph that would allow me to do this?Because if i want to make a heatmap out of it, I'll have to make a table with enhancers in rows and transcription factors in columns and I cant do that manually as I have a huge data list. My data looks like this:
Enhancer TF Gene1_Enhancer1 Arid3a Gene1_Enhnacer1 Ascl2 Gene1_Enhancer1 EBP Gene1_Enhancer2 ETS1 Gene2_Enhancer1 ETS1 Gene2_Enhancer1 Hltf Gene3_Enhancer1 Hoxa4 Gene3_Enhancer2 Hoxa7 Gene4_Enhancer1 Hoxa4
Thanks a lot!!!
Thanks a lot for your reply. I'm getting this error: Error in initFields(scales = scales) : could not find function "initRefFields"
Looks like an upgrade might be in your future: http://stackoverflow.com/questions/9863604/ggplot2-error-in-initfields . Could you post the output of sessionInfo()?
locale:  LCCOLLATE=EnglishUnited Kingdom.1252 LCCTYPE=EnglishUnited Kingdom.1252 LCMONETARY=EnglishUnited Kingdom.1252  LCNUMERIC=C LCTIME=English_United Kingdom.1252
attached base packages:  grid stats graphics grDevices utils datasets methods base
other attached packages:  gplots2.11.0 MASS7.3-16 KernSmooth2.23-6 caTools1.14 gdata2.12.0 gtools2.7.0 ggplot2_0.9.3
loaded via a namespace (and not attached): Error in x[["Version"]] : subscript out of bounds In addition: Warning message: In FUN(c("bitops", "colorspace", "dichromat", "digest", "gtable", : DESCRIPTION file of package 'digest' is missing or broken
Yep. You'll need to upgrade R. The stackoverflow post I noted above applies to you.
Thanks a lot!!! it works!