heatmap

data<-read.csv("/Bioinformatics/NGS_analyses/automated/RNA-Seq/Differential_Expression/20150905_DE_Analysis_ShinnyCho/comparison_1/NM_Vs_N_Filtered_Heatmap.csv",header=TRUE, row.names=1)

head(data)
data_matrix<-data.matrix(data)
head(data_matrix)
library("gplots")
library("RColorBrewer")


pdf("/Bioinformatics/NGS_analyses/automated/RNA-Seq/Differential_Expression/20150905_DE_Analysis_ShinnyCho/comparison_1/NM_Vs_N_Filtered_Heatmap.pdf")
heatmap.2(data_matrix, col=brewer.pal(11,"RdBu"),scale="row",trace="none")
dev.off()

data<-read.csv("/Bioinformatics/NGS_analyses/automated/RNA-Seq/Differential_Expression/20150905_DE_Analysis_ShinnyCho/comparison_1/NM_Vs_N_All_Heatmap.csv",header=TRUE, row.names=1)

head(data)
data_matrix<-data.matrix(data)
head(data_matrix)
library("gplots")
library("RColorBrewer")


pdf("/Bioinformatics/NGS_analyses/automated/RNA-Seq/Differential_Expression/20150905_DE_Analysis_ShinnyCho/comparison_1/NM_Vs_N_All_Heatmap.pdf")
heatmap.2(data_matrix, col=brewer.pal(11,"RdBu"),scale="row",trace="none")
dev.off()

kill user jobs

	Delete all your jobs (either will work, check different versions of PBS) qstat -u sudipto | awk -F. '/sudipto/{print $1}' | xargs qdel qstat | grep sudipto | awk -F. '{print $1}' | xargs qdel    Delete all your queued jobs only. Leaves all runnings jobs alone. qstat -u sudipto | awk -F. '/00 Q /{printf $1" "}' | xargs qdel qstat -u sudipto | awk -F. '/ Q --/{printf $1" " }' | xargs qdel   List all working nodes in the queue pbsnodes | egrep '^node|state =' | grep -B 1 'state = free' | grep ^node set NODELIST=`pbsnodes | egrep '^node|state =' | grep -B 1 'state = free' | grep ^node` foreach node ($NODELIST) /usr/local/torque-2.1.6/bin/qsub -l nodes=${NODE} ${HOME}/get.nodes.stats.csh done Run on a particular type of node qsub -l nodes=1:beta:ppn=1 ${script}