Creating plots mirrored along the y-axis

Good code example:

[code]#!/bin/bash ## Job Name #SBATCH...

## Job Name
#SBATCH --job-name=nl-02
## Allocation Definition
#SBATCH --account=coenv
#SBATCH --partition=coenv
## Resources
## Nodes (We only get 1, so this is fixed)
#SBATCH --nodes=1
## Walltime (days-hours:minutes:seconds format)
#SBATCH --time=20-00:00:00
## Memory per node
#SBATCH --mem=100G
#SBATCH --mail-type=ALL
## Specify the working directory for this job
#SBATCH --chdir=/gscratch/scrubbed/sr320/1009b/

module load ddocent.module

#source /gscratch/srlab/programs/scripts/

cd /gscratch/scrubbed/sr320/cragig_wd/

/gscratch/srlab/programs/dDocent-2.7.6/dDocent \

#sbatch, #source

Shelly’s Notebook: Thur. Oct. 3, Pt. Whitney Juvenile Geoduck var.low pH experiment

  • Got to the hatchery at 12:30
  • Had lab meeting from 12:30-1:15

Water chem

  • Water level in header tanks look normal. Last couple weeks it must have been a fluke, or perhaps related to low tide?
    Low pH header: uc?export=view&id=1ZbhTRaP733ENU08XPnchCwa4Wj8anAECambient header: uc?export=view&id=14MmxEBUwSBvIsM43YRST0fQ8xYOFIqdh
  • Took discrete measurements and TA at 3:40pm.
  • for TA, I took directly from the discrete measurment water after filtering it through 20uM. The discrete measurement water samples were directly from the headers and inside the silos (using clean TA cups). I poisoned samples to run at future time.
    • Discrete measurments looked as they should
    • I didn’t take measurments for volitional spawned low pH vs. ambient conditioned juveniles (from Sam’s summer experiment) because I was short on time.

animal check

Var.low pH treatment

ambient offspring:

  • 2.1: uc?export=view&id=1UkfsMqngRvpS-pI_6NiJSbfIjqt31gGa
  • 2.2: uc?export=view&id=1MSc0ef1YU2-l-qHSu_yL4ZjLgoO3ck9L
  • 2.3: uc?export=view&id=1clcxYbysOFRWIXkEuihZ7oCdR096ns6z
  • 2.4: uc?export=view&id=1IuPASSPJu-E_V5NvA5ckz0IcxbJopABX
  • 2.5: uc?export=view&id=1pCy7T5QrEXDTXeA6eT89J5GLlQoEXOG_

var.low pH offspring:

  • 2.8: uc?export=view&id=1w5T8QNKAMCwAP8Uo0rV7unGO-4eJU9IK
  • 2.10: uc?export=view&id=1XwjldKpHXI_p819lHWV3G2-fCNLfRwnE
  • 2.11: uc?export=view&id=1ID8842QDCpE8KoX5jUixGDvKhCPCqDQy
  • 2.12: uc?export=view&id=1pYkWuzZNvGQsM_C_-VsgViBrQcyYtzit

Ambient pH treatment

ambient offspring:

  • 3.1: uc?export=view&id=1g3QhE1wvOglEh7RG_tdEnEkJcI8bkUbN
  • 3.2: uc?export=view&id=1JAgl0tJ-V2K-8rDHCEYpRIWGCISj9eF7
  • 3.3: uc?export=view&id=18l_z6f-SV4LLpEs17HydL4MG8Uzlhf7F
  • 3.4: uc?export=view&id=1r0IwPuTEG89OLgojbUqTUhDiSd78FyBf

var.low pH offspring:

  • 3.8: uc?export=view&id=1-06hRZHSO6kA0cO4mSsmgWw5_YNUoBZP
  • 3.9: uc?export=view&id=1QLqZNPZXreCWpG1N4Qmcm4V7PJ0AXg8K
  • 3.10: uc?export=view&id=1JYkir0REv1JbAIMRisHY5cDXi4T_KrpD
  • 3.11: uc?export=view&id=1t24OHP-BgSVlZv4_LoHHMNr_KR4vjUT9
  • 3.12: uc?export=view&id=1uq3AVN_bEjtbdHAwM-Jws5dVopMZAOTJ

Sequim bay animals

  • 3.7: 1 mort. uc?export=view&id=1G0z2F_GIWlgrEfBQlvsXkJlj7FAvWHkx

Volitional spawned low pH vs. ambient conditioned juveniles (from Sam’s summer experiment)

  • H1T1 (low pH): uc?export=view&id=1uUSjKDKEw2wUF5lCExPcUvXPw7sTSelu
  • H1T2 (amb): uc?export=view&id=1zwFeJFQNjbW_T7X7eHIzzJWLWoJRHgKQ

System status

This is how things looked right before I left:

Low pH setup

  • uc?export=view&id=17muQJn2be8GQymch_y5NaFRjR9VS2M-Z
  • uc?export=view&id=1f8qW_5pEH1UDOuUI8gJgRV2ewiboR4f4

Amb. pH setup

  • uc?export=view&id=1vMSrx2MpHjaFukX0f7SQhettJBIAdpd9
  • uc?export=view&id=1NtM--LeOIfnrnJYXORgOCkNYhm5XbrKS


SDR plate order

  • uc?export=view&id=10YEeIo1aC_rsQisTbiulpoCC2o6BBdr5

Size photos

  • uc?export=view&id=1V6rvj0KsWOcu3pLh-VlIcZ1CnizSwMMq
    • I accidentally smashed the third column first row animal when getting it out of the vial 😦
  • more size photos are here

Data and analysis

  • I haven’t processed this yet, but will post soon.

Overall observations

  • Survival seems to be OK despite the empty shells on the surface. This is more obvious now that the animals are visibly growing.
  • Animals reared in the low pH condition show clear areas on their shells where perhaps calcium has been removed. Photos from the animal check and from the respirometry size photos show this.
  • Low pH conditioned animals appear larger than ambient conditioned, but many ambient animals are beneath the surface so this needs to be more thoroughly measured (which I’ll do in a couple weeks after 2 total months of conditioning). Besides the shell clearing, the low pH animals seem to look better than the ambient animals, but again that observation is disregarding animals that are buried.
  • It’s interesting that the low pH condition has more live animals hanging out on the surface compared to the ambient condition.

from shellytrigg