Graphical Exploratory Tools for ERP
Chi-Lin Yu
Outline
A reason workflow from user's perspective
Data
1. ERPdata : maybe a formal data for package
Preprocessing
1. data_select
2. data_summarize
3. downsample
EDA
1.edaplot
Data
head(dta[,1:5],3)
Channel value.1 value.2 value.3 value.4
1 Fp1 -1.545226 -1.889412 -1.463414 -1.335739
2 Fp2 -1.373787 -1.853133 -1.751572 -1.913380
3 F3 -2.856959 -2.690639 -0.926768 -0.168384
head(dta[,428:432],3)
Experiment Condition Subject AveRT IQ
1 Exp1 nonword subj1 0.01340599 65
2 Exp1 nonword subj1 0.01340599 65
3 Exp1 nonword subj1 0.01340599 65
Data
str(dta[,c(1:5,428:432)],digits.d=1)
'data.frame': 680 obs. of 10 variables:
$ Channel : Factor w/ 34 levels "Fp1","Fp2","F3",..: 1 2 3 4 5 6 7 8 9 10 ...
$ value.1 : num -2 -1 -3 -2 -5 ...
$ value.2 : num -2 -2 -3 -3 -5 ...
$ value.3 : num -1.5 -1.8 -0.9 -1.8 -2.4 ...
$ value.4 : num -1.3 -1.9 -0.2 -1.5 -1.3 ...
$ Experiment: chr "Exp1" "Exp1" "Exp1" "Exp1" ...
$ Condition : Factor w/ 2 levels "nonword","word": 1 1 1 1 1 1 1 1 1 1 ...
$ Subject : Factor w/ 10 levels "subj1","subj10",..: 1 1 1 1 1 1 1 1 1 1 ...
$ AveRT : num 0.01 0.01 0.01 0.01 0.01 ...
$ IQ : num 65 65 65 65 65 ...
Look at Data
timepoint <- seq(0,1700,by=4)
Fig1 <- edaplot(dta,
frames = timepoint ,
datacol=2:427,
subjcol=430,
chancol=1,
othvarcol=c(428:429,431:432),
select_subj=NULL,
select_chan=c("T3","T4","PZ"))+
geom_line(aes(col=Condition))+
facet_grid(Channel~Subject)
Look at Data
Look at Data
Fig2 <- edaplot(data = dta,
frames = timepoint ,
datacol=2:427,
subjcol=430,
chancol=1,
othvarcol=c(428:429,431:432),
select_subj=NULL,
select_chan="PZ",
outlinesub = "subj2",
outcolor = "red")+
facet_wrap(~Condition)
Fig3 <- edaplot(data = dta,
frames =timepoint ,
datacol=2:427,
subjcol=430,
chancol=1,
othvarcol=c(428:429,431:432),
select_subj=NULL,
select_chan="PZ",
outlinesub = "subj10",
outcolor = "blue")+
facet_wrap(~Condition)
Look at Data
Data Selection
dta2 <- data_select(data = dta,
frames = timepoint ,
datacol = 2:427,
subjcol = 430,
chancol = 1,
othvarcol = c(428:429,431:432),
select_subj = c(paste("subj",c(1,3:9),sep="")),
select_chan=c("T3","T4","PZ"))
head(dta2[,c(1,427:432)])
Channel value.426 Experiment Condition Subject AveRT IQ
1 T3 0.5572408 Exp1 nonword subj1 0.01340599 65
2 T3 6.7474460 Exp1 word subj1 0.09596096 65
3 T4 -10.0724000 Exp1 nonword subj1 0.01340599 65
4 T4 3.4233970 Exp1 word subj1 0.09596096 65
5 PZ -8.7248310 Exp1 nonword subj1 0.01340599 65
6 PZ 4.9487610 Exp1 word subj1 0.09596096 65
Downsample
dta3 <- downsample(data = dta2,
datacol = 2:427,
binwidth = 10, # 426/5 = 85.2
movinginterval=5)
timepoint2 <- seq(1,1700,by = 16.1)
Fig4 <- edaplot(data = dta3,
frames = timepoint2 ,
datacol= 7:112,
subjcol=4,
chancol=1,
othvarcol=c(2:3,5:6))+
geom_line(aes(col=Subject))+
facet_grid(Channel~Condition)
Downsample
Data Exploration
Fig5 <- edaplot(data = dta3,
frames = timepoint2 ,
datacol= 7:112,
subjcol=4,
chancol=1,
othvarcol=c(2:3,5:6))+
geom_line(aes(col=Condition))+
facet_grid(Channel~.)+
stat_summary(aes(group=Condition),fun.y = "mean",
colour = "purple", size = 1, geom = "point")+
theme_bw()+
theme(legend.position="bottom")+
labs(list(x="Signal",y="Time Points"))
Data Exploration
Data Exploration
Fig6 <- edaplot(data = dta3,
frames = timepoint2 ,
datacol= 7:112,
subjcol=4,
chancol=1,
othvarcol=c(2:3,5:6))+
geom_line(aes(col=IQ))+
facet_grid(Channel~.)+
scale_color_continuous(low="pink",high="red")+
theme_bw()
Data Exploration
Data Summarize
dtasum <- data_summarize(data=dta3,
frames = 1:426,
datacol = c(7:112,5),
subjcol = 4,
chancol = 1,
othvarcol = c(2:3,5:6),
summarycol= c(1,3),
fun=mean)
Fig7 <- edaplot(data = dtasum,
frames = timepoint2 ,
datacol= 3:108,
subjcol=NULL,
chancol=1,
othvarcol=c(2,109))+
geom_line(aes(col=Condition,size=as.factor(round(AveRT,1))))+
facet_grid(Channel~.)+
theme_bw()+
scale_size_discrete(name="Average RT",range=c(1,2))+
theme(legend.position="bottom")+
labs(list(title="Average ERP curve",x="Signal",y="Time Points"))
Data Exploration
Data
