dplot_al_map: dplot_al_map

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

dplot_al_map

Description

Plot an antennal lobe map with color coded odorant responses.

Usage

dplot_al_map(InChIKey,
  response_matrix = door_default_values("door_response_matrix"),
  odor_data = door_default_values("odor"),
  door_mappings = door_default_values("door_mappings"),
  zero = door_default_values("zero"),
  tag = door_default_values("tag.ALmap"), main = "Name",
  scalebar = door_default_values("scalebar"),
  door_AL_map = door_default_values("door_AL_map"),
  colors = door_default_values("colors"), legend = TRUE, limits,
  base_size = 12)

Arguments

InChIKey	InChIKey specifying the odorant to plot
response_matrix	the input data (e.g. door_response_matrix or door_response_matrix_non_normalized)
odor_data	data frame, contains the odorant information.
door_mappings	the data frame containing the mapping information
zero	the odorant to set to zero (defaults to "SFR")
tag	the labels to plot on top of the glomeruli (one of the following door_mappings columns: "receptor", "sensillum", "ORN", "glomerulus" or "co.receptor")
main	the title, one column of odor, defaults to "Name"
scalebar	whether or not to add a scalebar
door_AL_map	a list containing the AL model
colors	a vector containing 6 color values (2 for values below 0, 1 0 value and 3 steps between 0 and 1)
legend	logical, plot a legend?
limits	the limits for the color scale, if empty the range of the response matrix is taken (after setting “zero“ to 0)
base_size	numeric, the base font size for the ggplot plot

Details

Normalized, color coded odor responses across receptors are mapped onto a map of the Drosophila antennal lobe. The antennal lobe map was a kind gift from Veit Grabe.

Value

a ggplot2 object

Author(s)

Daniel Münch [e-mail]

Daniel Münch <[e-mail]>

References

Grabe, V., Strutz, A., Baschwitz, A., Hansson, B.S., Sachse, S., 2014. A digital in vivo 3D atlas of the antennal lobe of Drosophila melanogaster. J. Comp. Neurol. n/a–n/a. doi:10.1002/cne.23697

See Also

get_normalized_responses, ggplot2, grid

Examples

# load data
library(DoOR.data)
library(DoOR.functions)

# map responses on antennal lobe scheme
dplot_al_map("MLFHJEHSLIIPHL-UHFFFAOYSA-N", scalebar = FALSE)

# change colors
dplot_al_map("MLFHJEHSLIIPHL-UHFFFAOYSA-N", tag = "Ors",
   color = c("magenta", "pink", "white", "yellow", "orange", "red"))

# pass some ggplot2 theming parameters
dplot_al_map(trans_id("123-92-2"), scalebar = FALSE) +
ggplot2::theme(legend.position  = "bottom",
     panel.background = ggplot2::element_rect(fill = "grey90", color = NA)) +
ggplot2::ggtitle("responses elicited by isopentyl acetate")

# export as pdf
## Not run: 
p <- dplot_al_map(trans_id("123-92-2"))
ggplot2::ggsave("AL.response.pdf", p, width = 6, height = 2, scale = 2)

## End(Not run)

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