rforcancer

I hope the code here is fairly self-explanatory with the inset annotations. I feel this is just a bit 'prettier' than heatmap.2 and has for me the right balance of options and extensibility. I have also found it difficult to produce high quality plots with heatmap.2- whereas ggplots especially with RStudio assistance in resizing PNG turn out better IMHO.

## m=matrix(data=sample(rnorm(100,mean=0,sd=2)), ncol=10)
## this function makes a graphically appealing heatmap (no dendrogram) using ggplot
## whilst it contains fewer options than gplots::heatmap.2 I prefer its style and flexibility

I have published some initial script scribblings on this task about a week ago. After another week I'm posting some better formed and annotated code. The Biostrings and BSGenomes packages are new to me and I've gone through many many iterations and experimenations to arrive at the as yet incomplete code below. Whilst the packages seem powerful I'm yet to get the hang of the object structures and methods for the various DNAStrings, DNAStringSets, Views etc etc..-- and work out how best to functionally program with them.

I'm trying to search for binding sites for the transcription factor MAF (i.e. TFBS for MAF) in the promoter regions of various genes. I initially started out looking at a precomputed database of binding sites MAPPER. However the TFBS models that have been used from TRANSFAC or JASPAR are quite unlike the human binding sites  shown in the recent literature (the sites in the recent literature are palindromic sequences called MAREs).

Unfortunately the palindromic sites shown in the literature do not have alignment or position-weight-matrices (PWM) and they are quite variable.

I have just remembered a package called 'prettyR' that pretty much does what it says. It makes R code more readable.. so an example from my forthcoming genomeplot package (see forthcoming blog entry):

## this function integrates 3 steps to creating a genome plot
## 1 query bioMart to get a GFF like data-frame from ensembl
## 2 add new elements to the gff to make it plot with ggplot2
## 3 plot it with ggplot2
## the reason to split it like this is so that basic users may use this simple function
## and advanced users can try custom queries or altered plotting themes with the sep functions

I published the following on another blog Left Foot Forward.

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Recently the newspapers have been filled with apprehension at plans for a revolutionary decentralization of NHS management. Yet for NHS cancer services a similar experiment is well underway. The Interim Cancer Drug Fund (ICDF) is £50m of extra money (over 3 months) to purchase drugs that have been rejected or not yet approved by NICE. In contrast to the current system decisions on which treatments to offer are being made by local panels of clinicians within each Strategic Health Authority (SHA).

The MacMillan Cancer