In huangrh/blidata:

require(ggplot2)

# read the data 120420B
# channel B5: sensor=biotin-D1D2/8 micro-mole D1D2 in solusion
# channel C5: sensor=biotin-D1  /8 micro-mole D1D2
# channel D5: sensor=biotin-D2  /8 micro-mole D1D2
filePattern <- "RH120420B"
dirpath <- system.file("extdata", package = "blidata")
filelist <- file.path(dirpath,list.files(dirpath,pattern=filePattern))
datnames <- sapply(list.files(dirpath,pattern=filePattern),
                   simplify=TRUE, USE.NAMES=FALSE,
                   function(x) tools::file_path_sans_ext(x))
len <- length(datnames)
dats <- lapply(filelist, function(file){
    dat <- read.delim(file, skip=4, header=TRUE, sep="\t")})
dats <- setNames(dats,datnames)

plots <- sapply(dats, simplify=FALSE, function(dat){
    g <- radii:::ggplot()
    g <- g + geom_line(data=dat, aes(x=Time1,y=Data1))
    g <- g + xlab("Time (sec)") + ylab("R (nm)")
    g <- g + ggtitle("")
    g
})

# for (i in seq(1,6,by=2)) {
#     ggsave(filename=paste0("Fig01_",i,"s3.tiff"), 
#            plot=plots[[i]], dpi=300,
#            device="tiff", width=3,height=3 )}

# plot the second curve in the data
plots <- lapply(dats, function(dat){
    g <- radii:::ggplot()
    g <- g + geom_line(data=dat, aes(x=Time2, y=Data2))
    # print(g)
    g
})

# read the data 120615A
# channel A: control=biotin-BSA
# channel B: sensor =1 uM biotin-D2/D2, conc=0.16,,0.48,1.44,4.33,13uM
# channel C: sensor =2 uM biotin-D1/D2, conc=0.16,,0.48,1.44,4.33,13uM
filePattern <- "RH120615A"
dirpath <- system.file("extdata", package = "blidata")
filelist <- file.path(dirpath,list.files(dirpath,pattern=filePattern))
datnames <- sapply(list.files(dirpath,pattern=filePattern),
                   simplify=TRUE, USE.NAMES=FALSE,
                   function(x) tools::file_path_sans_ext(x))
len <- length(datnames)
dats <- lapply(filelist, function(file){
    # clean up the column name for the table
    colName <- read.delim(file, skip=1, nrow=1,header=F)
    colName <- colName[!is.na(colName)][-1]
    colName <- c("Time",paste(sprintf("%.3g",as.numeric(colName)*1e6)))

    # read the table
    dat <- read.delim(file, skip=4, header=TRUE, sep="\t")

    # clean up the table
    colKeep <- c(1,grep("Data",names(dat)))
    dat <- dat[colKeep]
    names(dat) <- colName

    # return the dat table
    return(dat)
    })

dats <- setNames(dats,datnames)
plots <- sapply(dats,simplify=FALSE,USE.NAMES=FALSE,
                function(dat){
                    # melt: wide table --> long table
                    dat <- reshape2::melt(data=dat,
                                          id.vars = 1,
                                          measure.vars = rev(2:ncol(dat)),
                                          variable.name="conc")
                    # draw the plot
                    g <- radii:::ggplot()
                    g <- g + geom_line(data=dat, aes(x=Time, y=value, col=conc))
                    g <- g + xlab("Time (sec)") + ylab("R (nm)") + ylim(-0.01,NA)
                    g
                } )

for (i in seq_along(plots)) {
    ggsave(filename=paste0("Fig01b_",i,"s4.tiff"), 
        plot=plots[[i]], dpi=300,
        device="tiff", width=4,height=3 )
}

huangrh/blidata documentation built on May 17, 2019, 9:10 p.m.