AJWillsey — May 24, 2013, 1:57 PM
#setwd("/Users/Spandrel/Dropbox/Statelab/CellPaper2013/syndromicAsSeeds/")
setwd("/Users/Canadia/Dropbox/Statelab/CellPaper2013/syndromicAsSeeds/")
#install.packages("RColorBrewer")
library("RColorBrewer")
#install.packages("gplots")
library(gplots)
Loading required package: gtools
Warning: package 'gtools' was built under R version 2.15.3
Loading required package: gdata
Warning: package 'gdata' was built under R version 2.15.1
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.
gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.
Attaching package: 'gdata'
The following object(s) are masked from 'package:stats':
nobs
The following object(s) are masked from 'package:utils':
object.size
Loading required package: caTools
Warning: package 'caTools' was built under R version 2.15.1
Loading required package: grid
Loading required package: KernSmooth
Warning: package 'KernSmooth' was built under R version 2.15.3
KernSmooth 2.23 loaded Copyright M. P. Wand 1997-2009
Loading required package: MASS
Warning: package 'MASS' was built under R version 2.15.1
Attaching package: 'gplots'
The following object(s) are masked from 'package:stats':
lowess
#read in file
mydata = read.table("syndromic_summary.txt", head=F, sep=" ", row.names=1);
##defined variables
single_lof=116;
total_genes=17573;
pval=as.data.frame(phyper(mydata[,1]-1, single_lof, total_genes-single_lof, mydata[,2], lower.tail=F))
#pval=pval*104
rownames(pval)=rownames(mydata)
periods=unlist(strsplit(rownames(pval), "-"))[seq(from=3, to=length(unlist(strsplit(rownames(pval), "-"))), by=5)]
periods=as.numeric(periods)
pval=cbind(periods, pval)
#pval=pval[pval[,1]!="all",]
pval=pval[order(rownames(pval)),]
pval
periods
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-1-3.iteration-syndromic.txt 1
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-10-12.iteration-syndromic.txt 10
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-11-13.iteration-syndromic.txt 11
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-12-14.iteration-syndromic.txt 12
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-13-15.iteration-syndromic.txt 13
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-2-4.iteration-syndromic.txt 2
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-3-5.iteration-syndromic.txt 3
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-4-6.iteration-syndromic.txt 4
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-5-7.iteration-syndromic.txt 5
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-6-8.iteration-syndromic.txt 6
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-7-9.iteration-syndromic.txt 7
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-8-10.iteration-syndromic.txt 8
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-9-11.iteration-syndromic.txt 9
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-1-3.iteration-syndromic.txt 1
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-10-12.iteration-syndromic.txt 10
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-11-13.iteration-syndromic.txt 11
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-12-14.iteration-syndromic.txt 12
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-13-15.iteration-syndromic.txt 13
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-2-4.iteration-syndromic.txt 2
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-3-5.iteration-syndromic.txt 3
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-4-6.iteration-syndromic.txt 4
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-5-7.iteration-syndromic.txt 5
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-6-8.iteration-syndromic.txt 6
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-7-9.iteration-syndromic.txt 7
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-8-10.iteration-syndromic.txt 8
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-9-11.iteration-syndromic.txt 9
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_syndromic.summary.top-20.windStart-1-3.iteration-syndromic.txt 1
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_syndromic.summary.top-20.windStart-10-12.iteration-syndromic.txt 10
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_syndromic.summary.top-20.windStart-11-13.iteration-syndromic.txt 11
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_syndromic.summary.top-20.windStart-12-14.iteration-syndromic.txt 12
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_syndromic.summary.top-20.windStart-13-15.iteration-syndromic.txt 13
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_syndromic.summary.top-20.windStart-2-4.iteration-syndromic.txt 2
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_syndromic.summary.top-20.windStart-3-5.iteration-syndromic.txt 3
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_syndromic.summary.top-20.windStart-4-6.iteration-syndromic.txt 4
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_syndromic.summary.top-20.windStart-5-7.iteration-syndromic.txt 5
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_syndromic.summary.top-20.windStart-6-8.iteration-syndromic.txt 6
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_syndromic.summary.top-20.windStart-7-9.iteration-syndromic.txt 7
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_syndromic.summary.top-20.windStart-8-10.iteration-syndromic.txt 8
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_syndromic.summary.top-20.windStart-9-11.iteration-syndromic.txt 9
new_autism.coexp.HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-1-3.iteration-syndromic.txt 1
new_autism.coexp.HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-10-12.iteration-syndromic.txt 10
new_autism.coexp.HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-11-13.iteration-syndromic.txt 11
new_autism.coexp.HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-12-14.iteration-syndromic.txt 12
new_autism.coexp.HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-13-15.iteration-syndromic.txt 13
new_autism.coexp.HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-2-4.iteration-syndromic.txt 2
new_autism.coexp.HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-3-5.iteration-syndromic.txt 3
new_autism.coexp.HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-4-6.iteration-syndromic.txt 4
new_autism.coexp.HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-5-7.iteration-syndromic.txt 5
new_autism.coexp.HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-6-8.iteration-syndromic.txt 6
new_autism.coexp.HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-7-9.iteration-syndromic.txt 7
new_autism.coexp.HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-8-10.iteration-syndromic.txt 8
new_autism.coexp.HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-9-11.iteration-syndromic.txt 9
new_autism.coexp.IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-1-3.iteration-syndromic.txt 1
new_autism.coexp.IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-10-12.iteration-syndromic.txt 10
new_autism.coexp.IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-11-13.iteration-syndromic.txt 11
new_autism.coexp.IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-12-14.iteration-syndromic.txt 12
new_autism.coexp.IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-13-15.iteration-syndromic.txt 13
new_autism.coexp.IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-2-4.iteration-syndromic.txt 2
new_autism.coexp.IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-3-5.iteration-syndromic.txt 3
new_autism.coexp.IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-4-6.iteration-syndromic.txt 4
new_autism.coexp.IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-5-7.iteration-syndromic.txt 5
new_autism.coexp.IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-6-8.iteration-syndromic.txt 6
new_autism.coexp.IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-7-9.iteration-syndromic.txt 7
new_autism.coexp.IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-8-10.iteration-syndromic.txt 8
new_autism.coexp.IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-9-11.iteration-syndromic.txt 9
new_autism.coexp.MD_CBC_syndromic.summary.top-20.windStart-1-3.iteration-syndromic.txt 1
new_autism.coexp.MD_CBC_syndromic.summary.top-20.windStart-10-12.iteration-syndromic.txt 10
new_autism.coexp.MD_CBC_syndromic.summary.top-20.windStart-11-13.iteration-syndromic.txt 11
new_autism.coexp.MD_CBC_syndromic.summary.top-20.windStart-12-14.iteration-syndromic.txt 12
new_autism.coexp.MD_CBC_syndromic.summary.top-20.windStart-13-15.iteration-syndromic.txt 13
new_autism.coexp.MD_CBC_syndromic.summary.top-20.windStart-2-4.iteration-syndromic.txt 2
new_autism.coexp.MD_CBC_syndromic.summary.top-20.windStart-3-5.iteration-syndromic.txt 3
new_autism.coexp.MD_CBC_syndromic.summary.top-20.windStart-4-6.iteration-syndromic.txt 4
new_autism.coexp.MD_CBC_syndromic.summary.top-20.windStart-5-7.iteration-syndromic.txt 5
new_autism.coexp.MD_CBC_syndromic.summary.top-20.windStart-6-8.iteration-syndromic.txt 6
new_autism.coexp.MD_CBC_syndromic.summary.top-20.windStart-7-9.iteration-syndromic.txt 7
new_autism.coexp.MD_CBC_syndromic.summary.top-20.windStart-8-10.iteration-syndromic.txt 8
new_autism.coexp.MD_CBC_syndromic.summary.top-20.windStart-9-11.iteration-syndromic.txt 9
new_autism.coexp.STR_HIP_AMY_syndromic.summary.top-20.windStart-1-3.iteration-syndromic.txt 1
new_autism.coexp.STR_HIP_AMY_syndromic.summary.top-20.windStart-10-12.iteration-syndromic.txt 10
new_autism.coexp.STR_HIP_AMY_syndromic.summary.top-20.windStart-11-13.iteration-syndromic.txt 11
new_autism.coexp.STR_HIP_AMY_syndromic.summary.top-20.windStart-12-14.iteration-syndromic.txt 12
new_autism.coexp.STR_HIP_AMY_syndromic.summary.top-20.windStart-13-15.iteration-syndromic.txt 13
new_autism.coexp.STR_HIP_AMY_syndromic.summary.top-20.windStart-2-4.iteration-syndromic.txt 2
new_autism.coexp.STR_HIP_AMY_syndromic.summary.top-20.windStart-3-5.iteration-syndromic.txt 3
new_autism.coexp.STR_HIP_AMY_syndromic.summary.top-20.windStart-4-6.iteration-syndromic.txt 4
new_autism.coexp.STR_HIP_AMY_syndromic.summary.top-20.windStart-5-7.iteration-syndromic.txt 5
new_autism.coexp.STR_HIP_AMY_syndromic.summary.top-20.windStart-6-8.iteration-syndromic.txt 6
new_autism.coexp.STR_HIP_AMY_syndromic.summary.top-20.windStart-7-9.iteration-syndromic.txt 7
new_autism.coexp.STR_HIP_AMY_syndromic.summary.top-20.windStart-8-10.iteration-syndromic.txt 8
new_autism.coexp.STR_HIP_AMY_syndromic.summary.top-20.windStart-9-11.iteration-syndromic.txt 9
phyper(mydata[, 1] - 1, single_lof, total_genes - single_lof, mydata[, 2], lower.tail = F)
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-1-3.iteration-syndromic.txt 0.0012081
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-10-12.iteration-syndromic.txt 0.3069995
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-11-13.iteration-syndromic.txt 0.0267381
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-12-14.iteration-syndromic.txt 0.1108430
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-13-15.iteration-syndromic.txt 0.3215727
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-2-4.iteration-syndromic.txt 0.1150536
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-3-5.iteration-syndromic.txt 0.3215727
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-4-6.iteration-syndromic.txt 0.1122398
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-5-7.iteration-syndromic.txt 0.1066940
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-6-8.iteration-syndromic.txt 0.0272396
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-7-9.iteration-syndromic.txt 0.1080701
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-8-10.iteration-syndromic.txt 0.2972519
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-9-11.iteration-syndromic.txt 0.3021285
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-1-3.iteration-syndromic.txt 0.0065456
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-10-12.iteration-syndromic.txt 0.3094327
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-11-13.iteration-syndromic.txt 0.0282594
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-12-14.iteration-syndromic.txt 0.6838151
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-13-15.iteration-syndromic.txt 0.0272396
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-2-4.iteration-syndromic.txt 0.0068549
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-3-5.iteration-syndromic.txt 0.6838151
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-4-6.iteration-syndromic.txt 0.0303666
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-5-7.iteration-syndromic.txt 0.1066940
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-6-8.iteration-syndromic.txt 0.3288328
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-7-9.iteration-syndromic.txt 0.6880169
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-8-10.iteration-syndromic.txt 0.0985871
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-9-11.iteration-syndromic.txt 0.2996908
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_syndromic.summary.top-20.windStart-1-3.iteration-syndromic.txt 0.0303666
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_syndromic.summary.top-20.windStart-10-12.iteration-syndromic.txt 0.3094327
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_syndromic.summary.top-20.windStart-11-13.iteration-syndromic.txt 0.6838151
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_syndromic.summary.top-20.windStart-12-14.iteration-syndromic.txt 0.3191484
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_syndromic.summary.top-20.windStart-13-15.iteration-syndromic.txt 0.1026082
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_syndromic.summary.top-20.windStart-2-4.iteration-syndromic.txt 0.3264149
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_syndromic.summary.top-20.windStart-3-5.iteration-syndromic.txt 0.6838151
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_syndromic.summary.top-20.windStart-4-6.iteration-syndromic.txt 0.1108430
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_syndromic.summary.top-20.windStart-5-7.iteration-syndromic.txt 0.3264149
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_syndromic.summary.top-20.windStart-6-8.iteration-syndromic.txt 0.3312484
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_syndromic.summary.top-20.windStart-7-9.iteration-syndromic.txt 0.6982810
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_syndromic.summary.top-20.windStart-8-10.iteration-syndromic.txt 0.0262423
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_syndromic.summary.top-20.windStart-9-11.iteration-syndromic.txt 0.3167223
new_autism.coexp.HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-1-3.iteration-syndromic.txt 0.0063947
new_autism.coexp.HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-10-12.iteration-syndromic.txt 0.1039631
new_autism.coexp.HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-11-13.iteration-syndromic.txt 0.3167223
new_autism.coexp.HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-12-14.iteration-syndromic.txt 0.3288328
new_autism.coexp.HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-13-15.iteration-syndromic.txt 0.0061003
new_autism.coexp.HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-2-4.iteration-syndromic.txt 0.0066990
new_autism.coexp.HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-3-5.iteration-syndromic.txt 0.6859230
new_autism.coexp.HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-4-6.iteration-syndromic.txt 0.1039631
new_autism.coexp.HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-5-7.iteration-syndromic.txt 0.3239949
new_autism.coexp.HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-6-8.iteration-syndromic.txt 0.3191484
new_autism.coexp.HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-7-9.iteration-syndromic.txt 0.6774069
new_autism.coexp.HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-8-10.iteration-syndromic.txt 0.0282594
new_autism.coexp.HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-9-11.iteration-syndromic.txt 0.0010135
new_autism.coexp.IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-1-3.iteration-syndromic.txt 0.0066990
new_autism.coexp.IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-10-12.iteration-syndromic.txt 0.0055403
new_autism.coexp.IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-11-13.iteration-syndromic.txt 0.0056768
new_autism.coexp.IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-12-14.iteration-syndromic.txt 1.0000000
new_autism.coexp.IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-13-15.iteration-syndromic.txt 0.3264149
new_autism.coexp.IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-2-4.iteration-syndromic.txt 0.0065456
new_autism.coexp.IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-3-5.iteration-syndromic.txt 0.3167223
new_autism.coexp.IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-4-6.iteration-syndromic.txt 0.3215727
new_autism.coexp.IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-5-7.iteration-syndromic.txt 0.1080701
new_autism.coexp.IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-6-8.iteration-syndromic.txt 0.3264149
new_autism.coexp.IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-7-9.iteration-syndromic.txt 0.1094531
new_autism.coexp.IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-8-10.iteration-syndromic.txt 0.0257520
new_autism.coexp.IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-9-11.iteration-syndromic.txt 0.0007926
new_autism.coexp.MD_CBC_syndromic.summary.top-20.windStart-1-3.iteration-syndromic.txt 0.0063947
new_autism.coexp.MD_CBC_syndromic.summary.top-20.windStart-10-12.iteration-syndromic.txt 0.0012432
new_autism.coexp.MD_CBC_syndromic.summary.top-20.windStart-11-13.iteration-syndromic.txt 0.3215727
new_autism.coexp.MD_CBC_syndromic.summary.top-20.windStart-12-14.iteration-syndromic.txt 1.0000000
new_autism.coexp.MD_CBC_syndromic.summary.top-20.windStart-13-15.iteration-syndromic.txt 0.3215727
new_autism.coexp.MD_CBC_syndromic.summary.top-20.windStart-2-4.iteration-syndromic.txt 0.1136433
new_autism.coexp.MD_CBC_syndromic.summary.top-20.windStart-3-5.iteration-syndromic.txt 0.0293017
new_autism.coexp.MD_CBC_syndromic.summary.top-20.windStart-4-6.iteration-syndromic.txt 0.3288328
new_autism.coexp.MD_CBC_syndromic.summary.top-20.windStart-5-7.iteration-syndromic.txt 0.0257520
new_autism.coexp.MD_CBC_syndromic.summary.top-20.windStart-6-8.iteration-syndromic.txt 0.0056768
new_autism.coexp.MD_CBC_syndromic.summary.top-20.windStart-7-9.iteration-syndromic.txt 0.6859230
new_autism.coexp.MD_CBC_syndromic.summary.top-20.windStart-8-10.iteration-syndromic.txt 0.1053250
new_autism.coexp.MD_CBC_syndromic.summary.top-20.windStart-9-11.iteration-syndromic.txt 0.1066940
new_autism.coexp.STR_HIP_AMY_syndromic.summary.top-20.windStart-1-3.iteration-syndromic.txt 0.1150536
new_autism.coexp.STR_HIP_AMY_syndromic.summary.top-20.windStart-10-12.iteration-syndromic.txt 0.6982810
new_autism.coexp.STR_HIP_AMY_syndromic.summary.top-20.windStart-11-13.iteration-syndromic.txt 1.0000000
new_autism.coexp.STR_HIP_AMY_syndromic.summary.top-20.windStart-12-14.iteration-syndromic.txt 0.1150536
new_autism.coexp.STR_HIP_AMY_syndromic.summary.top-20.windStart-13-15.iteration-syndromic.txt 0.3336616
new_autism.coexp.STR_HIP_AMY_syndromic.summary.top-20.windStart-2-4.iteration-syndromic.txt 0.3288328
new_autism.coexp.STR_HIP_AMY_syndromic.summary.top-20.windStart-3-5.iteration-syndromic.txt 0.1122398
new_autism.coexp.STR_HIP_AMY_syndromic.summary.top-20.windStart-4-6.iteration-syndromic.txt 1.0000000
new_autism.coexp.STR_HIP_AMY_syndromic.summary.top-20.windStart-5-7.iteration-syndromic.txt 1.0000000
new_autism.coexp.STR_HIP_AMY_syndromic.summary.top-20.windStart-6-8.iteration-syndromic.txt 0.1150536
new_autism.coexp.STR_HIP_AMY_syndromic.summary.top-20.windStart-7-9.iteration-syndromic.txt 1.0000000
new_autism.coexp.STR_HIP_AMY_syndromic.summary.top-20.windStart-8-10.iteration-syndromic.txt 0.6982810
new_autism.coexp.STR_HIP_AMY_syndromic.summary.top-20.windStart-9-11.iteration-syndromic.txt 1.0000000
mymatrix=as.data.frame(rep("NA", dim(pval)[1]/13));
rownames(mymatrix)=gsub("_ASD_windStart-[1-9][1-3]{0,1}", "", rownames(pval[pval[,1]==1,]))
for(i in 1:13){
temp <- as.data.frame(pval[pval[,1]==i,][,2]);
colnames(temp)=i;
tmpRowNames=rownames(pval[pval[,1]==i,])
rownames(temp)=gsub("_ASD_windStart-[1-9][1-3]{0,1}", "", tmpRowNames)
mymatrix<-cbind(mymatrix, temp);
}
mymatrix=mymatrix[,-1]
mymatrix=t(mymatrix)
mymatrix=mymatrix*91
#all analyzed - clustered by time period, scaled by column
mylogdata=apply(mymatrix, c(1,2), log10)
mylogdata[which(mylogdata>0)]=0
mylogdata=apply(mylogdata, c(1,2), abs)
mylogdata=mylogdata[,c(1, 2, 4, 3, 5, 6, 7)]
mylogdata
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-1-3.iteration-syndromic.txt
1 0.9588
2 0.0000
3 0.0000
4 0.0000
5 0.0000
6 0.0000
7 0.0000
8 0.0000
9 0.0000
10 0.0000
11 0.0000
12 0.0000
13 0.0000
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-1-3.iteration-syndromic.txt
1 0.225
2 0.205
3 0.000
4 0.000
5 0.000
6 0.000
7 0.000
8 0.000
9 0.000
10 0.000
11 0.000
12 0.000
13 0.000
new_autism.coexp.HIP_AMY_STR_MD_CBC_syndromic.summary.top-20.windStart-1-3.iteration-syndromic.txt
1 0.2351
2 0.2150
3 0.0000
4 0.0000
5 0.0000
6 0.0000
7 0.0000
8 0.0000
9 1.0351
10 0.0000
11 0.0000
12 0.0000
13 0.2556
new_autism.coexp.DFC_VFC_MFC_OFC_M1C_S1C_syndromic.summary.top-20.windStart-1-3.iteration-syndromic.txt
1 0
2 0
3 0
4 0
5 0
6 0
7 0
8 0
9 0
10 0
11 0
12 0
13 0
new_autism.coexp.IPC_A1C_STC_ITC_V1C_syndromic.summary.top-20.windStart-1-3.iteration-syndromic.txt
1 0.2150
2 0.2250
3 0.0000
4 0.0000
5 0.0000
6 0.0000
7 0.0000
8 0.0000
9 1.1419
10 0.2974
11 0.2869
12 0.0000
13 0.0000
new_autism.coexp.MD_CBC_syndromic.summary.top-20.windStart-1-3.iteration-syndromic.txt
1 0.2351
2 0.0000
3 0.0000
4 0.0000
5 0.0000
6 0.2869
7 0.0000
8 0.0000
9 0.0000
10 0.9464
11 0.0000
12 0.0000
13 0.0000
new_autism.coexp.STR_HIP_AMY_syndromic.summary.top-20.windStart-1-3.iteration-syndromic.txt
1 0
2 0
3 0
4 0
5 0
6 0
7 0
8 0
9 0
10 0
11 0
12 0
13 0
newNames=c("All brain", "Neocortical", "Non-neocortical", "Frontal cortex (+S1C)", "ITC, IPC, A1C, STC, V1C", "MD, CBC", "STR, HIP, AMY")
colnames(mylogdata)=newNames
rownames(mylogdata)=c("1-3", "2-4", "3-5", "4-6", "5-7", "6-8", "7-9", "8-10", "9-11", "10-12", "11-13", "12-14", "13-15")
##color pallette
pbreaks=seq(min(mylogdata), max(mylogdata), 0.5)
color.palette=colorRampPalette(c("#FFFFFF","#AD0C17"))(length(pbreaks)-1)
x=mylogdata
x=round(x,digits=1)
x[x<=0]<-""
setEPS()
postscript(file="syndromic_heatmap.eps", width=4.25, height=5, paper="special", colormodel="srgb", horizontal=FALSE)
par(mfcol=c(1,1), mai=c(0, 0, 0.5 ,0.75), omi=c(0,0,0,0.25), ps=12, font.lab=2, font.main=2,
mgp=c(2.75, 0.5, 0), las=1, cex=1, cex.lab=1, cex.main=1, cex.axis=1)
heatmap.2(mylogdata, Colv=NULL, Rowv=NULL, scale="none", cexCol=1, main="", margin=c(12,2),
col=color.palette, key=F, trace="none", dendrogram="none", revC=T, ylab="",
xlab="Brain regions examined", density.info="none", cellnote=x,
ps=12, font.lab=2, font.main=2, colsep=c(3), sepcolor="black",
lmat=rbind( c(4, 3), c(2,1) ),lwid=c(0.1,1), lhei=c(0.1,1) )
Error: figure margins too large
dev.off()
pdf
2
#plot for notebook
heatmap.2(mylogdata, Colv=NULL, Rowv=NULL, scale="none", cexCol=1, main="", margin=c(12,4),
col=color.palette, key=F, trace="none", dendrogram="none", revC=T, ylab="",
xlab="Brain regions examined", density.info="none", cellnote=x,
ps=12, font.lab=2, font.main=2, colsep=c(3), sepcolor="black",
lmat=rbind( c(4, 3), c(2,1) ),lwid=c(0.1,1), lhei=c(0.1,1) )
Error: figure margins too large