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andschar merged 2 commits into from
Sep 22, 2025
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Hannes dev #15

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ec38454
Added README.html
hreinwald Sep 22, 2025
8e78fff
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hreinwald Sep 22, 2025
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2 changes: 1 addition & 1 deletion .gitignore
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Expand Up @@ -6,4 +6,4 @@
*.Rproj
*.ini
tests/*
R/my_custom_fun.R
R/my_custom_fun.R
8 changes: 5 additions & 3 deletions R/standartox.R
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Expand Up @@ -373,7 +373,7 @@ stx_query = function(
# Split up list object
total_entries = nrow(stxDb$test_fin)
tox.dt = stxDb$test_fin # final output object. LARGE right after import!
suppressWarnings( tox.dt[, casnr := NULL] ) # HOT FIX!
suppressWarnings( tox.dt[, cl_id := NULL] ) # HOT FIX!
stxDb = stxDb[stx_table[-1]] # dump the largest object! <- hope to save some memory with that.

# First quick filter steps:
Expand Down Expand Up @@ -410,9 +410,11 @@ stx_query = function(
if( nrow(stxDb$phch) == 0 ) {
warning("No query matches found for the provided CAS numbers. Please check the input values.")
}
merge(stxDb$phch, tox.dt, all.x = TRUE, by = "cl_id") -> tox.dt
#merge(stxDb$phch, tox.dt, all.x = TRUE, by = "cl_id") -> tox.dt
merge(stxDb$phch, tox.dt, all.x = TRUE, by = "casnr") -> tox.dt
} else {
merge(stxDb$phch, tox.dt, all.y = TRUE, by = "cl_id") -> tox.dt
#merge(stxDb$phch, tox.dt, all.y = TRUE, by = "cl_id") -> tox.dt
merge(stxDb$phch, tox.dt, all.y = TRUE, by = "casnr") -> tox.dt
}
suppressWarnings( tox.dt[, c("chem_class","casnr", "cl_id") := NULL] ) # don't need the cl_id column anymore.

Expand Down
33 changes: 7 additions & 26 deletions README.Rmd
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Expand Up @@ -12,13 +12,9 @@ Standartox is a database and tool facilitating the retrieval of ecotoxicological

## Installation

**_NOTE:_** Currently v0.0.2 is only available here on GitHub.

```{r eval=FALSE}
# install.packages('standartox') # Currently only available on GitHub
if (!requireNamespace("standartox", quietly = TRUE)) {
remotes::install_github('andschar/standartox') # development version
}
# install.packages('standartox') # CRAN Server version
remotes::install_github('andschar/standartox') # Github version
```

## Functions
Expand Down Expand Up @@ -81,33 +77,18 @@ We subset the retrieved data to the 20 most tested chemicals and plot the result
```{r warning=FALSE, message=FALSE}
cas20 = oncor[ , .N, cas ][ order(-N) ][1:20]
oncor20 = oncor[ cas %in% cas20$cas ]
# add new column which combines chem_name & cas
oncor20[ , chem_name := paste0(chem_name, ' [CAS: ', cas, ']') ]
gmn_dt = oncor20[ , .(gmn = exp(mean(log(concentration), na.rm = TRUE))), .(cas, chem_name, tax_genus)]
# add new column which combines common_name & cas
oncor20[ , new_chem_name := paste0(common_name, ' [CAS: ', cas, ']') ]
gmn_dt = oncor20[ , .(gmn = exp(mean(log(concentration), na.rm = TRUE))), .(cas, new_chem_name, tax_genus)]
```

```{r warning=FALSE, message=FALSE, fig.width=9, fig.height=6, dpi=300}
require(ggplot2)
# ggplot(oncor20, aes(y = cas)) +
# geom_point(aes(x = concentration, col = 'All values'),
# pch = 1, alpha = 0.3) +
# geom_point(data = gmn_dt,
# aes(y = reorder(cas, -gmn), x = gmn, col = 'Standartox value\n(Geometric mean)'),
# size = 3) +
# scale_x_log10(breaks = c(0.01, 0.1, 1, 10, 100, 1000, 10000),
# labels = c(0.01, 0.1, 1, 10, 100, 1000, 10000)) +
# scale_color_viridis_d(name = '') +
# labs(title = 'LC50 values for Genus: Oncorhynchus',
# subtitle = '20 most tested chemicals',
# x = 'Concentration [g/L]') +
# theme_minimal() +
# theme(axis.title.y = element_blank())

ggplot(oncor20, aes(y = chem_name)) +
ggplot(oncor20, aes(y = new_chem_name)) +
geom_point(aes(x = concentration, col = 'All values'),
pch = 1, alpha = 0.3) +
geom_point(data = gmn_dt,
aes(y = reorder(chem_name, -gmn), x = gmn, col = 'Standartox value\n(Geometric mean)'),
aes(y = reorder(new_chem_name, -gmn), x = gmn, col = 'Standartox value\n(Geometric mean)'),
size = 3) +
scale_x_log10(breaks = c(0.01, 0.1, 1, 10, 100, 1000, 10000),
labels = c(0.01, 0.1, 1, 10, 100, 1000, 10000)) +
Expand Down
69 changes: 31 additions & 38 deletions README.html
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68 changes: 29 additions & 39 deletions README.md
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Expand Up @@ -18,13 +18,9 @@ environmental toxicity of chemicals.

## Installation

***NOTE:*** Currently v0.0.2 is only available here on GitHub.

``` r
# install.packages('standartox') # Currently only available on GitHub
if (!requireNamespace("standartox", quietly = TRUE)) {
remotes::install_github('andschar/standartox') # development version
}
# install.packages('standartox') # CRAN Server version
remotes::install_github('andschar/standartox') # Github version
```

## Functions
Expand All @@ -48,16 +44,16 @@ catal = stx_catalog()
names(catal)
```

## [1] "date_compiled" "standartox_version" "cas" "chem_class"
## [5] "cname" "ref_author" "ref_number" "ref_title"
## [9] "ref_year" "class" "continent" "family"
## [13] "genus" "group" "habitat" "order"
## [17] "rank" "taxon" "casnr" "cl_id"
## [21] "concentration" "concentration_orig" "concentration_type" "concentration_unit"
## [25] "concentration_unit_orig" "duration" "duration_orig" "duration_unit"
## [29] "duration_unit_orig" "effect" "endpoint" "endpoint_group"
## [33] "exposure" "qualifier" "ref_number" "result_id"
## [37] "tl_id"
## [1] "cas" "casnr" "chem_class" "chem_name"
## [5] "ref_author" "ref_number" "ref_title" "ref_year"
## [9] "tax_class" "tax_continent" "tax_family" "tax_genus"
## [13] "tax_group" "tax_habitat" "tax_order" "tax_rank"
## [17] "tax_taxon" "casnr" "cl_id" "concentration"
## [21] "concentration_orig" "concentration_type" "concentration_unit" "concentration_unit_orig"
## [25] "duration" "duration_orig" "duration_unit" "duration_unit_orig"
## [29] "effect" "endpoint" "endpoint_group" "exposure"
## [33] "measurement" "organism_lifestage" "qualifier" "ref_number"
## [37] "result_id" "tl_id"

``` r
catal$endpoint # access the parameter top five endpoints
Expand All @@ -67,16 +63,16 @@ Showing the top 10 endpoint values from `stx_catalog()`

| n | variable |
|-------:|:---------|
| 202306 | NOEL |
| 191672 | NR |
| 162103 | LOEL |
| 152748 | NOEC |
| 135906 | LC50 |
| 113089 | LOEC |
| 53417 | EC50 |
| 22027 | BCF |
| 17337 | NR-LETH |
| 16179 | LD50 |
| 205080 | NOEL |
| 196597 | NR |
| 165693 | LOEL |
| 165146 | NOEC |
| 143740 | LC50 |
| 123889 | LOEC |
| 56362 | EC50 |
| 22496 | BCF |
| 17739 | NR-LETH |
| 16213 | LD50 |

### `stx_query()`

Expand All @@ -93,16 +89,13 @@ more detail.

## Reading in Standartox Data ...

## fstcore package v0.10.0

## (OpenMP detected, using 8 threads)

## Removing rows with 'NR' (not reported) for endpoint & duration_unit ...

## Appending chemical information ...

## Appending taxonomic information ...

## Query returned 801451 results out of 1212683 total entries.
## Done!

## Example: *Oncorhynchus*
Expand Down Expand Up @@ -138,6 +131,7 @@ oncor = stx_query(

## Appending taxonomic information ...

## Query returned 3178 results out of 1212683 total entries.
## Done!

We subset the retrieved data to the 20 most tested chemicals and plot
Expand All @@ -146,18 +140,18 @@ the result.
``` r
cas20 = oncor[ , .N, cas ][ order(-N) ][1:20]
oncor20 = oncor[ cas %in% cas20$cas ]
# add new column which combines cname & cas
oncor20[ , cname := paste0(cname, ' [CAS: ', cas, ']') ]
gmn_dt = oncor20[ , .(gmn = exp(mean(log(concentration), na.rm = TRUE))), .(cas, cname, tax_genus)]
# add new column which combines common_name & cas
oncor20[ , new_chem_name := paste0(common_name, ' [CAS: ', cas, ']') ]
gmn_dt = oncor20[ , .(gmn = exp(mean(log(concentration), na.rm = TRUE))), .(cas, new_chem_name, tax_genus)]
```

``` r
require(ggplot2)
ggplot(oncor20, aes(y = cname)) +
ggplot(oncor20, aes(y = new_chem_name)) +
geom_point(aes(x = concentration, col = 'All values'),
pch = 1, alpha = 0.3) +
geom_point(data = gmn_dt,
aes(y = reorder(cname, -gmn), x = gmn, col = 'Standartox value\n(Geometric mean)'),
aes(y = reorder(new_chem_name, -gmn), x = gmn, col = 'Standartox value\n(Geometric mean)'),
size = 3) +
scale_x_log10(breaks = c(0.01, 0.1, 1, 10, 100, 1000, 10000),
labels = c(0.01, 0.1, 1, 10, 100, 1000, 10000)) +
Expand All @@ -171,10 +165,6 @@ ggplot(oncor20, aes(y = cname)) +

![](README_files/figure-gfm/unnamed-chunk-8-1.png)<!-- -->

``` r
# Antimycin A (CAS 1397-94-0) listed as NA in standartox! Need to check this ...
```

## Article

The article on Standartox is published
Expand Down
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