JaderaRNAi: Shape data from _Jadera haematoloma_ RNAi specimens
In aphanotus/borealis: Tools for reproducible geometric morphometric analysis

JaderaRNAi

R Documentation

Shape data from Jadera haematoloma RNAi specimens

Description

Coordinate shape data from the dorsal side of red-shouldered soapberry bugs, Jadera haematoloma produced through RNA interference experiments.

Usage

JaderaRNAi

Format

An object of class list of length 6.

Details

coords: An array of XY coordinates for the shape of multiple specimens (42 landmarks by 2 (XY) by 141 specimens).
landmark.number: The number of landmarks in the shape data.
specimen.number: The number of specimens in the shape data.
metadata: A data frame of metadata.
provenance: Data provenance.

Metadata includes the following

id: An ID name for each specimen, which combines a unique identifer with the dsRNA target, morph and sex.
treatment: An arbitary treatment ID number.
dsRNA: The dsRNA target sequence GFP = green flourescent protein (the dsRNA sequence control). FoxO = Forkhead Box Class O. EGF = Epidermal Growth Factor (Keren). EGFR = EGF Receptor. ERK = Extracellular signal-regulated kinase (rolled).
pop: The population of origin. SP = Silver Palm Dr, Miami, FL. KL = Key Largo, FL. LE = Leesburg, FL. AC = Aurora, CO. FR = Frederick, MD PK = Plantation Key, FL.
hostplant: The host plant bugs were collected from in the wild, or reared on in the lab. GRT = goldenrain tree, Koelreuteria sp. BV = balloon vine, Cardiospermum corindum.
vol: The volume of the container used to house the bugs after dsRNA injection (L).
seeds: The number of seeds caged with the cohort during the bug's rearing. (Only available for lab-raised bugs.)
cohort: The number of conspecifics present in the cohort during the bug's rearing. (Only available for lab-raised bugs.)
morph: Whether the bug was classified as long winged (LW) oir short-winged (SW).
sex: Whether the bug is female (f) or male (m).
digitizer: The initials of the person who did the landmark digitization.
daid: Dorsal anterior inter-ocular distance: the distance distance across the head, measured from the dorsal view, just anterior of the eyes (mm).
pronutum: The maximum width of the pronotum (mm).
winglength: The length of the upper wing, from the edge of the pronotum to its distal tip (mm).
bodylength: The length of the body, from clypeus to terminalia, measured from the ventral side (mm).
beak: The length of the beak (also called the rostrum or labium), from anterior of the clypeus to its distal tip (mm).
labrum: The length of the labrum, from anterior of the clypeus to its distal tip (mm).
antenna: The mean length of the antennae (mm).
femur1: The mean length of the femur of the first legs (mm).
femur2: The mean length of the femur of the second legs (mm).
femur3: The mean length of the femur of the third legs (mm).

Source

Dave Angelini david.r.angelini@gmail.com [aut, cre]

References

Fawcett, M.M., Parks, M.C., Tibbetts, A.E., Swart, J.S., Richards, E.M., Vanegas, J.C., Cenzer, M., Crowley, L., Simmons, W.R., Hou, W.S., Angelini, D.R. (2018). Manipulation of insulin signaling phenocopies evolution of a host-associated polyphenism. Nature Communications 9: 1699. https://doi.org/10.1038/s41467-018-04102-1

Liou, C., Swart, J.S., Angelini, D.R. (unpublished) Effects of EGF pathway knockdown on wing shapes in Jadera haematoloma

Examples

# Load the dataset
data("JaderaRNAi", package = "borealis")

# Define connecting lines
{
  x <- 1:9
  jhae.lines <- matrix(c(x[-length(x)], x[length(x)], x[-1], x[1]), ncol = 2)
  x <- c(10,11,17,16,15,12,13,14)
  jhae.lines <- rbind(jhae.lines, matrix(c(x[-length(x)], x[length(x)], x[-1], x[1]), ncol = 2) )
  x <- c(17,18,15,16)
  jhae.lines <- rbind(jhae.lines, matrix(c(x[-length(x)], x[length(x)], x[-1], x[1]), ncol = 2) )
  x <- c(19,21,22,20,26,25,32:34,31,35:39,29,40:42)
  jhae.lines <- rbind(jhae.lines, matrix(c(x[-length(x)], x[length(x)], x[-1], x[1]), ncol = 2) )
  x <- c(19,23, 23,24, 23,28, 28,29, 19,24, 24,27, 27,28, 19,25, 27,30)
  jhae.lines <- rbind(jhae.lines, matrix(x, ncol = 2, byrow = TRUE) )
  x <- c(1,3, 7,9, 14,16, 16,18)
  jhae.lines <- rbind(jhae.lines, matrix(x, ncol = 2, byrow = TRUE) )
}

landmark.plot(JaderaRNAi, links = jhae.lines)
landmark.plot(JaderaRNAi, links = jhae.lines, specimen.number = c(9:10,21:22))

aphanotus/borealis documentation built on Nov. 4, 2022, 8:44 p.m.