SVG images

[Aariq]

Before I forget and I lose this train of thought / link again, I wanted to mention that gt can pretty easily display SVG images where the SVG is stored as a character column in a data frame. I can't remember which if any webchem functions can return SVGs, but having the SVG as just text in the returned tibble might be a cool option.

There's some example code (not using webchem) from a workshop I ran here. This is what the output looks like:

[Aariq]

Oh yeah, and gt now has gt::fmt_chem() too. Might be nice to get webchem to play nicely with gt and create a vignette for creating tables like this.

[Aariq]

@jranke — meant to tag you in this since you mentioned interest in displaying images

[jranke]

Thanks for the tip! This will come in handy with my collection of SVG images created using RDKit in the chents package.

[stitam]

Thanks @Aariq, this is great!

I looked at the webchem functions, I think all functions that generate images have _img() suffix. I found two such functions,cir_img() (exports png or gif) and cs_img() (exports png). We can get to SVG files if we use e.g. cs_compinfo(id, fields = "Mol3D") to get a mol string, export it using write_mol(), then import the mol file with an external software e.g. Avogadro, and export is as SVG. I wouldn't call this streamlined :) Maybe we should look for an implementation for exporting mol objects as svg?

[jranke]

Some similar code using chents and RDKit would look like this

library(chents)
library(purrr)
library(tibble)
library(gt)

# Get SMILES from PubChem, internally using webchem,
# and SVG, internally using RDKit
chemicals <- c("caffeine", "vanillin")
chent_list <- map(chemicals, \(x) chent$new(x))
#> PubChem:
#> Trying to get chemical information from RDKit using PubChem_Canonical SMILES
#> CN1C=NC2=C1C(=O)N(C(=O)N2C)C
#> Did not find chyaml file ./caffeine.yaml
#> PubChem:
#> Trying to get chemical information from RDKit using PubChem_Canonical SMILES
#> COC1=C(C=CC(=C1)C=O)O
#> RDKit mw is 152.149
#> mw is 152.15
#> Did not find chyaml file ./vanillin.yaml

# Make a table with name, SMILES and svg
chent_table <- map(chent_list, 
  \(x) {
    tibble(name = x$identifier,
           SMILES = x$smiles,
           svg = x$svg)
  })  |>
  list_rbind()

# Show table 
print(chent_table)
#> # A tibble: 2 × 3
#>   name     SMILES                       svg                                     
#>   <chr>    <chr>                        <chr>                                   
#> 1 caffeine CN1C=NC2=C1C(=O)N(C(=O)N2C)C "<?xml version='1.0' encoding='iso-8859…
#> 2 vanillin COC1=C(C=CC(=C1)C=O)O        "<?xml version='1.0' encoding='iso-8859…

# Display structure of first element using the chent plot method
plot(chent_list[[1]])

# I was expecting this to work, too, but it does not
gt(chent_table) |>
  fmt_markdown(columns = svg)

<style>#brjbnrgaqz table { font-family: system-ui, 'Segoe UI', Roboto, Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol', 'Noto Color Emoji'; -webkit-font-smoothing: antialiased; -moz-osx-font-smoothing: grayscale; }

#brjbnrgaqz thead, #brjbnrgaqz tbody, #brjbnrgaqz tfoot, #brjbnrgaqz tr, #brjbnrgaqz td, #brjbnrgaqz th {
border-style: none;
}

#brjbnrgaqz p {
margin: 0;
padding: 0;
}

#brjbnrgaqz .gt_table {
display: table;
border-collapse: collapse;
line-height: normal;
margin-left: auto;
margin-right: auto;
color: #333333;
font-size: 16px;
font-weight: normal;
font-style: normal;
background-color: #FFFFFF;
width: auto;
border-top-style: solid;
border-top-width: 2px;
border-top-color: #A8A8A8;
border-right-style: none;
border-right-width: 2px;
border-right-color: #D3D3D3;
border-bottom-style: solid;
border-bottom-width: 2px;
border-bottom-color: #A8A8A8;
border-left-style: none;
border-left-width: 2px;
border-left-color: #D3D3D3;
}

#brjbnrgaqz .gt_caption {
padding-top: 4px;
padding-bottom: 4px;
}

#brjbnrgaqz .gt_title {
color: #333333;
font-size: 125%;
font-weight: initial;
padding-top: 4px;
padding-bottom: 4px;
padding-left: 5px;
padding-right: 5px;
border-bottom-color: #FFFFFF;
border-bottom-width: 0;
}

#brjbnrgaqz .gt_subtitle {
color: #333333;
font-size: 85%;
font-weight: initial;
padding-top: 3px;
padding-bottom: 5px;
padding-left: 5px;
padding-right: 5px;
border-top-color: #FFFFFF;
border-top-width: 0;
}

#brjbnrgaqz .gt_heading {
background-color: #FFFFFF;
text-align: center;
border-bottom-color: #FFFFFF;
border-left-style: none;
border-left-width: 1px;
border-left-color: #D3D3D3;
border-right-style: none;
border-right-width: 1px;
border-right-color: #D3D3D3;
}

#brjbnrgaqz .gt_bottom_border {
border-bottom-style: solid;
border-bottom-width: 2px;
border-bottom-color: #D3D3D3;
}

#brjbnrgaqz .gt_col_headings {
border-top-style: solid;
border-top-width: 2px;
border-top-color: #D3D3D3;
border-bottom-style: solid;
border-bottom-width: 2px;
border-bottom-color: #D3D3D3;
border-left-style: none;
border-left-width: 1px;
border-left-color: #D3D3D3;
border-right-style: none;
border-right-width: 1px;
border-right-color: #D3D3D3;
}

#brjbnrgaqz .gt_col_heading {
color: #333333;
background-color: #FFFFFF;
font-size: 100%;
font-weight: normal;
text-transform: inherit;
border-left-style: none;
border-left-width: 1px;
border-left-color: #D3D3D3;
border-right-style: none;
border-right-width: 1px;
border-right-color: #D3D3D3;
vertical-align: bottom;
padding-top: 5px;
padding-bottom: 6px;
padding-left: 5px;
padding-right: 5px;
overflow-x: hidden;
}

#brjbnrgaqz .gt_column_spanner_outer {
color: #333333;
background-color: #FFFFFF;
font-size: 100%;
font-weight: normal;
text-transform: inherit;
padding-top: 0;
padding-bottom: 0;
padding-left: 4px;
padding-right: 4px;
}

#brjbnrgaqz .gt_column_spanner_outer:first-child {
padding-left: 0;
}

#brjbnrgaqz .gt_column_spanner_outer:last-child {
padding-right: 0;
}

#brjbnrgaqz .gt_column_spanner {
border-bottom-style: solid;
border-bottom-width: 2px;
border-bottom-color: #D3D3D3;
vertical-align: bottom;
padding-top: 5px;
padding-bottom: 5px;
overflow-x: hidden;
display: inline-block;
width: 100%;
}

#brjbnrgaqz .gt_spanner_row {
border-bottom-style: hidden;
}

#brjbnrgaqz .gt_group_heading {
padding-top: 8px;
padding-bottom: 8px;
padding-left: 5px;
padding-right: 5px;
color: #333333;
background-color: #FFFFFF;
font-size: 100%;
font-weight: initial;
text-transform: inherit;
border-top-style: solid;
border-top-width: 2px;
border-top-color: #D3D3D3;
border-bottom-style: solid;
border-bottom-width: 2px;
border-bottom-color: #D3D3D3;
border-left-style: none;
border-left-width: 1px;
border-left-color: #D3D3D3;
border-right-style: none;
border-right-width: 1px;
border-right-color: #D3D3D3;
vertical-align: middle;
text-align: left;
}

#brjbnrgaqz .gt_empty_group_heading {
padding: 0.5px;
color: #333333;
background-color: #FFFFFF;
font-size: 100%;
font-weight: initial;
border-top-style: solid;
border-top-width: 2px;
border-top-color: #D3D3D3;
border-bottom-style: solid;
border-bottom-width: 2px;
border-bottom-color: #D3D3D3;
vertical-align: middle;
}

#brjbnrgaqz .gt_from_md > :first-child {
margin-top: 0;
}

#brjbnrgaqz .gt_from_md > :last-child {
margin-bottom: 0;
}

#brjbnrgaqz .gt_row {
padding-top: 8px;
padding-bottom: 8px;
padding-left: 5px;
padding-right: 5px;
margin: 10px;
border-top-style: solid;
border-top-width: 1px;
border-top-color: #D3D3D3;
border-left-style: none;
border-left-width: 1px;
border-left-color: #D3D3D3;
border-right-style: none;
border-right-width: 1px;
border-right-color: #D3D3D3;
vertical-align: middle;
overflow-x: hidden;
}

#brjbnrgaqz .gt_stub {
color: #333333;
background-color: #FFFFFF;
font-size: 100%;
font-weight: initial;
text-transform: inherit;
border-right-style: solid;
border-right-width: 2px;
border-right-color: #D3D3D3;
padding-left: 5px;
padding-right: 5px;
}

#brjbnrgaqz .gt_stub_row_group {
color: #333333;
background-color: #FFFFFF;
font-size: 100%;
font-weight: initial;
text-transform: inherit;
border-right-style: solid;
border-right-width: 2px;
border-right-color: #D3D3D3;
padding-left: 5px;
padding-right: 5px;
vertical-align: top;
}

#brjbnrgaqz .gt_row_group_first td {
border-top-width: 2px;
}

#brjbnrgaqz .gt_row_group_first th {
border-top-width: 2px;
}

#brjbnrgaqz .gt_summary_row {
color: #333333;
background-color: #FFFFFF;
text-transform: inherit;
padding-top: 8px;
padding-bottom: 8px;
padding-left: 5px;
padding-right: 5px;
}

#brjbnrgaqz .gt_first_summary_row {
border-top-style: solid;
border-top-color: #D3D3D3;
}

#brjbnrgaqz .gt_first_summary_row.thick {
border-top-width: 2px;
}

#brjbnrgaqz .gt_last_summary_row {
padding-top: 8px;
padding-bottom: 8px;
padding-left: 5px;
padding-right: 5px;
border-bottom-style: solid;
border-bottom-width: 2px;
border-bottom-color: #D3D3D3;
}

#brjbnrgaqz .gt_grand_summary_row {
color: #333333;
background-color: #FFFFFF;
text-transform: inherit;
padding-top: 8px;
padding-bottom: 8px;
padding-left: 5px;
padding-right: 5px;
}

#brjbnrgaqz .gt_first_grand_summary_row {
padding-top: 8px;
padding-bottom: 8px;
padding-left: 5px;
padding-right: 5px;
border-top-style: double;
border-top-width: 6px;
border-top-color: #D3D3D3;
}

#brjbnrgaqz .gt_last_grand_summary_row_top {
padding-top: 8px;
padding-bottom: 8px;
padding-left: 5px;
padding-right: 5px;
border-bottom-style: double;
border-bottom-width: 6px;
border-bottom-color: #D3D3D3;
}

#brjbnrgaqz .gt_striped {
background-color: rgba(128, 128, 128, 0.05);
}

#brjbnrgaqz .gt_table_body {
border-top-style: solid;
border-top-width: 2px;
border-top-color: #D3D3D3;
border-bottom-style: solid;
border-bottom-width: 2px;
border-bottom-color: #D3D3D3;
}

#brjbnrgaqz .gt_footnotes {
color: #333333;
background-color: #FFFFFF;
border-bottom-style: none;
border-bottom-width: 2px;
border-bottom-color: #D3D3D3;
border-left-style: none;
border-left-width: 2px;
border-left-color: #D3D3D3;
border-right-style: none;
border-right-width: 2px;
border-right-color: #D3D3D3;
}

#brjbnrgaqz .gt_footnote {
margin: 0px;
font-size: 90%;
padding-top: 4px;
padding-bottom: 4px;
padding-left: 5px;
padding-right: 5px;
}

#brjbnrgaqz .gt_sourcenotes {
color: #333333;
background-color: #FFFFFF;
border-bottom-style: none;
border-bottom-width: 2px;
border-bottom-color: #D3D3D3;
border-left-style: none;
border-left-width: 2px;
border-left-color: #D3D3D3;
border-right-style: none;
border-right-width: 2px;
border-right-color: #D3D3D3;
}

#brjbnrgaqz .gt_sourcenote {
font-size: 90%;
padding-top: 4px;
padding-bottom: 4px;
padding-left: 5px;
padding-right: 5px;
}

#brjbnrgaqz .gt_left {
text-align: left;
}

#brjbnrgaqz .gt_center {
text-align: center;
}

#brjbnrgaqz .gt_right {
text-align: right;
font-variant-numeric: tabular-nums;
}

#brjbnrgaqz .gt_font_normal {
font-weight: normal;
}

#brjbnrgaqz .gt_font_bold {
font-weight: bold;
}

#brjbnrgaqz .gt_font_italic {
font-style: italic;
}

#brjbnrgaqz .gt_super {
font-size: 65%;
}

#brjbnrgaqz .gt_footnote_marks {
font-size: 75%;
vertical-align: 0.4em;
position: initial;
}

#brjbnrgaqz .gt_asterisk {
font-size: 100%;
vertical-align: 0;
}

#brjbnrgaqz .gt_indent_1 {
text-indent: 5px;
}

#brjbnrgaqz .gt_indent_2 {
text-indent: 10px;
}

#brjbnrgaqz .gt_indent_3 {
text-indent: 15px;
}

#brjbnrgaqz .gt_indent_4 {
text-indent: 20px;
}

#brjbnrgaqz .gt_indent_5 {
text-indent: 25px;
}

#brjbnrgaqz .katex-display {
display: inline-flex !important;
margin-bottom: 0.75em !important;
}

#brjbnrgaqz div.Reactable > div.rt-table > div.rt-thead > div.rt-tr.rt-tr-group-header > div.rt-th-group:after {
height: 0px !important;
}
</style>

name	SMILES	svg
caffeine	CN1C=NC2=C1C(=O)N(C(=O)N2C)C
vanillin	COC1=C(C=CC(=C1)C=O)O

^{Created on 2024-12-09 with reprex v2.1.1}