You can control what is output from code chunks by changing knitr options. options are described here in detail.
Below some of the options I most use are shown.
eval=FALSE will turn the code evaluation off. The code still will be shown.
with eval=TRUE
summary(cars)
## speed dist
## Min. : 4.0 Min. : 2
## 1st Qu.:12.0 1st Qu.: 26
## Median :15.0 Median : 36
## Mean :15.4 Mean : 43
## 3rd Qu.:19.0 3rd Qu.: 56
## Max. :25.0 Max. :120
with eval=FALSE
summary(cars)
You can supress warnings in the code output by setting warning=FALSE
warning=TRUE
cor(c(1, 1, 1), c(1, 1, 1))
## Warning: the standard deviation is zero
## [1] NA
warning=FALSE
cor(c(1, 1, 1), c(1, 1, 1))
## [1] NA
You can suppress messages from the code by setting message=FALSE
message=TRUE
library(GenomicRanges)
## Loading required package: BiocGenerics Loading required package: parallel
##
## Attaching package: 'BiocGenerics'
##
## The following objects are masked from 'package:parallel':
##
## clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport,
## clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply,
## parSapply, parSapplyLB
##
## The following object is masked from 'package:stats':
##
## xtabs
##
## The following objects are masked from 'package:base':
##
## anyDuplicated, as.data.frame, cbind, colnames, duplicated, eval, Filter,
## Find, get, intersect, lapply, Map, mapply, match, mget, order, paste,
## pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int,
## rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist
##
## Loading required package: IRanges
message=FALSE for the R chunk.
library(GenomicRanges)
plot(cars)
You can also execute code but hide the figures with fig.show='hide' option for the R chunk.
plot(cars)
summary(cars)
## speed dist
## Min. : 4.0 Min. : 2
## 1st Qu.:12.0 1st Qu.: 26
## Median :15.0 Median : 36
## Mean :15.4 Mean : 43
## 3rd Qu.:19.0 3rd Qu.: 56
## Max. :25.0 Max. :120