I\'m pretty much a beginner at programmatically formatting R output, but I\'ve got a basic understanding of knitr, xtable, Markdown, and Pandoc\'s
Well, not using colors (as not supported by markdown), but you can highlight cells/rows/columns of the table with pandoc.table and the general pander method by using bold or italics font face:
> library(pander)
> emphasize.rows(which(df$outcome == 2))
> pander(df)
-------------------------
id inputval outcome
---- ---------- ---------
29 0.89 1
*79* *0.69* *2*
*41* *0.64* *2*
*89* *1* *2*
95 0.66 1
5 0.71 1
53 0.54 1
*90* *0.6* *2*
*56* *0.29* *2*
46 0.14 4
96 0.97 1
*46* *0.91* *2*
68 0.69 4
58 0.8 1
11 0.02 3
90 0.48 1
25 0.76 1
5 0.21 4
33 0.32 4
*96* *0.23* *2*
-------------------------