The main purpose of the
dbparser package is to parse the DrugBank database which is downloadable in XML format from this link. The parsed data can then be explored and analyzed as desired by the user. In this tutorial, we will see how to use
dbparser along with
ggplot2 along with other libraries to do simple drug analysis
Before starting the code we are assuming the following:
Now we can loads the
drug groups info and
drug targets actions info.
## load dbparser package library(dbparser) library(dplyr) library(ggplot2) library(XML) ## parse data from XML and save it to memory read_drugbank_xml_db("C:\drugbank.xml") ## load drugs data drugs <- drug() ## load drug groups data drug_groups <- drug_groups() ## load drug targets actions data drug_targets_actions <- targets_actions()
User can save parsed tibbles in database by enabling
save_table option. More details about that can be found in database tutorial
Following is an example involving a quick look at a few aspects of the parsed data. First we look at the proportions of
small-molecule drugs in the data.
Below, we view the different
drug_groups in the data and how prevalent they are.
## view proportions of the different drug types for each drug group drugs %>% full_join(drug_groups, by = c('primary_key' = 'drugbank_id')) %>% select(type, group) %>% ggplot(aes(x = group, fill = type)) + geom_bar() + theme(legend.position = 'bottom') + labs(x = 'Drug Group', y = 'Quantity', title = "Drug Type Distribution per Drug Group", caption = "created by ggplot") + coord_flip()
Finally, we look at the
drug_targets_actions to observe their proportions as well.
## get counts of the different target actions in the data targetActionCounts <- drug_targets_actions %>% group_by(action) %>% summarise(count = n()) %>% arrange(desc(count)) ## get bar chart of the 10 most occurring target actions in the data p <- ggplot(targetActionCounts[1:10,], aes(x = reorder(action,count), y = count, fill = letters[1:10])) + geom_bar(stat = 'identity') + labs(fill = 'action', x = 'Target Action', y = 'Quantity', title = 'Target Actions Distribution', subtitle = 'Distribution of Target Actions in the Data', caption = 'created by ggplot') + guides(fill = FALSE) + ## removes legend for the bar colors coord_flip() ## switches the X and Y axes ## display plot p