View source: R/hits_by_groupings.R
hits_by_groupings_DT | R Documentation |
The hits_by_groupings_DT
(DT option) and
hits_by_groupings
(data frame option) functions create tables
with one row per category("Biological", "Chemical", or "Chemical Class").
The columns indicate the "Biological" groupings. The values in the table
signify how many sites have samples with EARs that exceeded the hit_threshold
for that particular "Biological"/category combination. If the user chooses
"Biological" as the category, it is a simple 2-column table of "Biological"
groupings and number of sites (nSites).
hits_by_groupings_DT(
chemical_summary,
category = "Biological",
mean_logic = FALSE,
sum_logic = TRUE,
hit_threshold = 0.1
)
hits_by_groupings(
chemical_summary,
category,
mean_logic = FALSE,
sum_logic = TRUE,
hit_threshold = 0.1
)
chemical_summary |
Data frame from |
category |
Character. Either "Biological", "Chemical Class", or "Chemical". |
mean_logic |
Logical. |
sum_logic |
Logical. |
hit_threshold |
Numeric threshold defining a "hit". |
The tables result in slightly different results for a single site, displaying the number of samples with hits rather than the number of sites.
data frame with one row per category, and one column per Biological grouping.
# This is the example workflow:
path_to_tox <- system.file("extdata", package = "toxEval")
file_name <- "OWC_data_fromSup.xlsx"
full_path <- file.path(path_to_tox, file_name)
tox_list <- create_toxEval(full_path)
ACC <- get_ACC(tox_list$chem_info$CAS)
ACC <- remove_flags(ACC)
cleaned_ep <- clean_endPoint_info(end_point_info)
filtered_ep <- filter_groups(cleaned_ep)
chemical_summary <- get_chemical_summary(tox_list, ACC, filtered_ep)
site_df <- hits_by_groupings(chemical_summary, category = "Biological")
hits_by_groupings_DT(chemical_summary, category = "Biological")
hits_by_groupings_DT(chemical_summary, category = "Chemical Class")
hits_by_groupings_DT(chemical_summary, category = "Chemical")
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