Merge pull request #62 from wgerlach/master

updated usage
Update group_stats_plot.r

cut 
, row.names = rownames(my_stats.summary)
from line 155 -- was incorrect(labeled sorted data with unsorted labels - dough); default behavior should be correct.
decompress test for the SHOCK based inbox
Merge pull request #63 from paczian/master

decompress test for the SHOCK based inbox
fix ko->ss script
subsystems now outputs SSid and role
Merge pull request #64 from teharrison/master

fixes
Update plot_mg_heatdend.r
Update plot_mg_heatdend.r

made sure R calls the matR version of the heatmap function
fix kegg2ss tool
Merge branch 'master' of github.com:MG-RAST/MG-RAST-Tools
Merge pull request #65 from teharrison/master

fix kegg2ss tool
Update plot_mg_pcoa.r

added option to select distance metric
Update plot_mg_pcoa.r
Create rename_columns.r

New function to rename columns in data file with any column from the metadata file
Update plot_mg_heatdend.r

added scale factors for row and column labels
Merge branch 'master' of github.com:MG-RAST/MG-RAST-Tools
added distance metric to pcoa plot
added intersection filtering: filter function matrix by taxaon and vice-versa
Merge pull request #66 from teharrison/master

update pcoa and abundace profile scripts with more options