identify_sensillum: identify_sensillum

In ropensci/DoOR.functions: Integrating Heterogeneous Odorant Response Data into a Common Response Model: A DoOR to the Complete Olfactome

identify_sensillum

Description

correlates the result from a SSR recording of several odorants against all DoOR response profiles

Usage

identify_sensillum(recording,
  response_matrix = door_default_values("door_response_matrix"),
  odor_data = door_default_values("odor"),
  door_mappings = door_default_values("door_mappings"), tag = "Name",
  min.cor = 0.9, nshow = 10, method = "cor", sub, base_size = 12,
  plot = TRUE, use = "everything")

Arguments

recording	data frame, a data frame with the following columns "odorants" containing InChIKeys of the tested odorrant, and one column called "unit1" etc. for each unit, containing responses (or estimates) scaled between 0 and 1 (see examples)
response_matrix	DoOR response matrix, the data to compair against
odor_data	data frame, contains the odorant information.
door_mappings	the data frame containing the mapping information
tag	character, the chemical identifier to use in plots, one of colnames(odor)
min.cor	numeric, a minimum correlation value, the function will check wether there is a higher correlation for all units within a single sensillum
nshow	numeric, the number of plots to nshow, plot e.g. only the top 10 matches
method	character, the method for similarity calculations: correlation ("cor") or Euclidean distances ("dist")
sub	character, if you know the class of sensillum you were recording from you can restrict the search to this subset here ("ab", "ac", "at", "pb", "sac")
base_size	numeric, the base font size of the ggplot plots
plot	logical, if TRUE returns the plot, else returns the data frame with the correlations/distances
use	character, the "use" option from the cor function, "all" returns NA when pairs are incomplete, "na.or.complete" only uses complete observations to calculate correlations; see cor for details

Value

eithe& Carolin G.(†27)r a plot (gtable) with responses sorted by highest correlations or lowest distances, or a data frame containing all calculated correlations or Euclidean distances

Author(s)

Daniel Münch <[e-mail]>

Examples

# load data
library(DoOR.data)

# create an example recording
recording <- data.frame(
   odorants = c(trans_id(c("BEDN", "ETAS"), "Code"),
   trans_id("carbon dioxide", "Name")),
   unit1 = c(.9,.1,.1),
   unit2 = c(0, .1, 1)
)

# run the identification
identify_sensillum(recording)
identify_sensillum(recording, method = "dist", nshow = 5)

ropensci/DoOR.functions documentation built on Feb. 22, 2024, 9:44 a.m.