This is an example of how to use knitr for producing reports on data stored in Opal.
The requirement on client side is to have opal package installed:
install.packages('opal', repos=c(getOption('repos'), 'http://cran.obiba.org'), dependencies=TRUE)
The requirements on server side is:
The procedure is then the following:
Load the required libraries on client side and login in Opal (credentials and output are hidden)...
library(opal) o <- opal.login('administrator', 'password', 'https://opal-demo.obiba.org')
Assign some variables into a data.frame with associated D symbol in R on Opal server side:
opal.assign(o,'D','FNAC.FNAC',variables=c('SVUOSI','SUKUP','PITUUS','PAINO'))
Preview the assigned data.frame:
opal.execute(o,'head(D)')
Summary of the assigned data.frame:
opal.execute(o,'summary(D)')
Histogram figure of the PITUUS variable:
plot(opal.execute(o,'hist(D$PITUUS)'))
Loading ggplot2 library in R on Opal server side... This will fail if ggplot2 is not installed in R server environment.
opal.execute(o, 'library(ggplot2)')
Plot PITUUS vs. PAINO with "lm" smoothing:
opal.execute(o,'qplot(PITUUS,PAINO, data=D) + geom_smooth(method="lm")')
Cleaning the resources on Opal server side...
opal.logout(o)
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