Query the PubChem api and retrieve a display an image of the matching molecular structure.
Usage
pubchem_structure(
query_column,
search_by,
row_index,
record_type = "2d",
image_size = "large",
...
)Arguments
- query_column
(character) The name of the
annotation_sourcecolumn with compound identifiers of the type specified in thesearch_byparam.- search_by
(character) The PubChem domain to search for matches to the annotation_column.
- row_index
(integer, numeric) The row index of the
annotation_sourceto request an image of the molecular structure of.- record_type
(character) The record type to return from the PubChem query. Can be one of "2d" or "3d". The default is
"2d".- image_size
(character) The size of the image to return from the PubChem query. Can be one of "large" or "small". For
record_type = "2d"an arbitrary image size can be specified e.g.123x123. The default is"large".- ...
Additional slots and values passed to
struct_class.
Value
A
pubchem_structure
object. This object has no output slots.
See chart_plot in the struct package to
plot this chart object.
Details
This object makes use of functionality from the following packages:
cowplot
This object queries the PubChem API for matches to your query without caching the results. It is therefore intended for limited use. If you wish to obtain images for a large number of moelucules you should seek an alternative solution.
Inheritance
A pubchem_structure object inherits the following struct classes:
[pubchem_structure] -> [chart] -> [struct_class]
References
Wilke C (2024). cowplot: Streamlined Plot Theme and Plot Annotations for 'ggplot2'. R package version 1.1.3, https://CRAN.R-project.org/package=cowplot.