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dplot_al_map

Source: R/dplot_al_map.R
dplot_al_map.Rd

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

Value

a ggplot2 object

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.

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

Author

Daniel Münch daniel.muench@uni-konstanz.de

Daniel Münch <daniel.muench@uni-konstanz.de>

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"))
#> Warning: Removed 2 rows containing missing values or values outside the scale range
#> (`geom_text()`).


# 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
if (FALSE) { # \dontrun{
p <- dplot_al_map(trans_id("123-92-2"))
ggplot2::ggsave("AL.response.pdf", p, width = 6, height = 2, scale = 2)
} # }