bar_slct: Extract data.frame and barplot

In shkonishi/rsko: This is my personal package of R functions

Extract data.frame and barplot

Description

Extract data.frame and barplot

Usage

bar_slct(dat, mrgn, slct, target, pm, nm, yscale, gg, wrapcol, xlb, ylb, ...)

Arguments

dat	data.frame
mrgn	integer 1 or 2 search row is 1, search col is 2
slct	character
target	character
pm	character strings. A type of pattern match, as 'mgrep', 'mmatch', or 'match'. The default value is 'mmatch'
nm	character vector, as name of labels of barplot. If it is 'NULL', names or rownames of data.frame will used as 'nm'.
yscale	character 'free' or 'fixed'. The default value is 'free'
gg	logical default value is FALSE
wrapcol	integer
xlb	character
ylb	character
...	other barplot options

Examples

## Not run: 
# sample data
zdat <- rsko::zconv(iris, -5, 1)
nfpkm <- rskodat::nfpkm[1:36,]
kodat <- rskodat::kodat
cpdat <- rskodat::cpdat
cge100 <- rskodat::cge100

# search strings
slct1 <- c('1', '51', '101')
slct2 <- c('gene1', 'gene10', 'gene150')
slct3 <- c('K07230', 'K02030', 'K02073')
slct4 <- c('100770489', '100689463', '100774853')

# subset rows of data.frame
par(mar=c(6, 4, 2, 1), mfrow=c(1,3))
res1 <- rsko::bar_slct(zdat[-5], mrgn=1, slct=slct1, target=rownames(zdat), yscale='fixed')
res2 <- rsko::bar_slct(zdat[-5], mrgn=1, slct=slct1, target=rownames(zdat), yscale='fixed', gg=TRUE)
print(res2)

# subset columns of data.frame
res3 <- rsko::bar_slct(dat=nfpkm[-1:-4], mrgn=2, slct=slct2,
 target=names(nfpkm[-1:-4]), nm=nfpkm$id)
res4 <- rsko::bar_slct(dat=nfpkm[-1:-4], mrgn=2, slct=slct2,
 target=names(nfpkm[-1:-4]), gg=TRUE, xlb = 'sample', ylb = 'fpkm')

# subset rows of data.frame
par(mfrow=c(1,3))
res4 <- rsko::bar_slct(dat=kodat, mrgn=1, slct=slct3, target=rownames(kodat))
res5 <- rsko::bar_slct(dat=kodat, mrgn=1, slct=slct3, target=rownames(kodat), yscale='fixed')
res6 <- rsko::bar_slct(dat=kodat, mrgn=1, slct=slct3, target=rownames(kodat), gg=TRUE,
                 yscale = 'fixed', wrapcol=3, xlb='condition', ylb='relative exp.')

# partial match of search strings　
res7 <- rsko::bar_slct(dat=cge100, mrgn=1, slct=slct4, target=rownames(cge100),
                 pm = 'mgrep', yscale = 'fixed')

# result of degview genes
res.degv <- rskodat::res.degv
res8 <- lapply(1:nrow(res.degv), function(i){
                  subg <- unlist(strsplit(unlist(res.degv[i, 'kos']), ';'))
                  rsko::bar_slct(dat=kodat, mrgn=1, slct=subg, yscale = 'fixed',
                  target=rownames(kodat), gg=TRUE)
                  })
# result of degview cpds
res9 <- lapply(1:nrow(res.degv), function(i){
                  subg <- unlist(strsplit(unlist(res.degv[i, 'cpds']), ';'))
                  rsko::bar_slct(dat=cpdat, mrgn=1, slct=subg, target=rownames(cpdat),
                                 yscale = 'fixed', gg=TRUE)
                  })

## End(Not run)

shkonishi/rsko documentation built on Feb. 21, 2023, 5:12 a.m.