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Geochemistry pipeline for processing and visualising data from IRMS, IC and ICP-MS

Home Page: https://github.com/giovannellilab/geochem

License: Other

R 91.88% TeX 8.12%

geochemistry microbiology

geochem's Introduction

geochem

Geochemistry pipeline for processing and visualising data from IRMS, IC and ICP-MS.

Installation

Installation of the package and its dependencies can be done either using a conda environment or directly in R.

Option 1: Install using R

devtools::install_github("giovannellilab/geochem", dependencies=TRUE, build_vignettes=TRUE)

Option 2: Install using a conda environment

Creating a conda environment simplifies having different R and packages versions. It is strongly recommended to create an environment and install all required packages in there.

conda create -n geochem -y

# NOTE: for Macs with M1/M2 chips
CONDA_SUBDIR=osx-64 conda create -n geochem -y

Installation of dependencies:

conda activate geochem
conda install r-base r-essentials r-ggtern r-rio r-devtools r-svglite -y

IMPORTANT: if you use RStudio you need to launch it from the terminal with the activated conda environment:

conda activate geochem
rstudio

Installation of the geochem package can then be done by running the following code in R:

devtools::install_github("giovannellilab/geochem", build_vignettes=TRUE)

Usage

For a detailed pipeline, please refer to the geochem vignette. You can display it after installation via:

vignette("geochem")

Processing ICP-MS data

Refer to the ICP-MS section in the geochem vignette, in which the process is detailed.

geochem's People

Contributors

Watchers

geochem's Issues

Add lines and ticks to axes (ternary plots)

Fix behaviour of process_icp_data function

Fix sample name: avoid dilutions in it and information about replicates (those should be in other columns)
Remove filling in the SD with RSD values (assume we will have replicates and they will have exactly the same sample name)
Remove RSD rows since we are not using them
~~Remove CPS checks since we are not checking them~~

Create docs

Check correct calculation of values in the Giggenbach plot for cations

Add Durov plot

Check this paper

Add process arrows to Langelier-Ludwig plot

Make SD checks independent of scale

Fix replicates IDs in ICP-MS data before processing them

For example, if there are two replicates for the same sample (e.g. labelled _1 and _2), remove the replicate label and process them together.

Create one plot for each metal

Customization of LL plot

Adding an option to increase the size of the points
Adding the code outside the function to customize coloring the points by a set of variables

Add Duchi et al. 1995 ternary cations plot

Add explanations to README and template notebook

Specify format for ICP sample names (PROJECT_SAMPLE_1inDILUTION_REPLICATE)
Specify folder architecture for the data

Add ternary plot for He-Ar-N

Check PER22 data

Create GitHub workflow

Add CO2 vs He plot

Check this function.
Check all different plots in the paper and add them

Use GLab theme in all plots

Position labels on top of the points for all plots

Change DIC plot to boxplot per sample and color all gray

Save SVG instead of PNG files

Add PCA analysis to notebook

Fix metals plot

Add the parameter to use log or percentage
Remove [ppb] from axis
Add absolute stacked bar plot on top of this one (check geom_col)
Set blank as the first sample

Fix warning messages in IC plots

Add ternary plot for CO2-He3-He

Rename Giggenbach cations to maturity plot

Add parameters in plots for coloring by variable (temperature, pH, etc.)

Rename areas in Giggenbach anions plot

Modify notebook to work with env_data templates

Add major cations ternary plot in Fullerton et al. 2021

Create unit tests

Use only meq in all plots

Custom Piper Plot

Create piper plot from scratch without using the SMWR package
Define/customize the color palette for the piper plot

Convert new IC values from ppm to meq

Calculate meq
For bicarbonate, multiply by 1.22

Add contour lines to all points

Remove elements from ICP-MS raw data

Remove the following metals from the list:
Li [He] and Li [No Gas]
Na [ No Gas ]
Mg [ No Gas ] and Mg [ He ]
P [ No Gas ]
S [ No Gas ]
K [ No Gas ] and K [ He ]
Ca [ He ] and Ca [ No Gas ] and
Si [ No Gas ]

Change the color palette

"#2E83AD",
"#66C2A5",
"#ABD9E9",
"#E6F598",
"#FFFFBF",
"#FEE08B",
"#FDAE61",
"#F46D43",
"#D53E4F", --> Co
"#9E0142",
"#8E0152",
"#C51B7D", --> Cu
"#DE77AE",
"#F1B6DA",
"#FDE0EF",
"#e08214", --> Fe
"#F7F7F7",
"#D9F0D3",
"#A6DBA0",
"#5AAE61",
"#1B7837", --> Mn
"#00441B", -->Mo
"#4D9221",
"#7CB85C", --> Ni
"#A6D96A",
"#D9EF8B",
"#FFFFCC",
"#FDAE61",
"#F46D43", --> Se
"#D73027",
"#A50026",
"#67001F",
"#EF8A62",
"#F7F7F7",
"#67A9CF",
"#D0E1F0",
"#FFFFB3",
"#F0F0F0",
"#B3DE69", --> V
"#8DD3C7",--> W
"#80B1D3",
"#5E4FA2",
"#BEBADA",
"#FDB462",--> Zn
"#FB8072"

Filter metals in ICP-MS plot

Fix location of labels in Giggenbach anions plot

Force NA when calculating standard deviation with some values as NA

Fix mature waters area in Giggenbach anions plot

Add ternary plot (Giggenbach) for anions

Change line colors in Piper plot to gray

Fix calculation of dilution change

Change text color to gray

Correct colnames for the IC

Change the colnames of the IC data to match the colnames from the env_dataset template of the Glab

Add plot for delta-13C vs delta-15N

Add checks for sample selection

Check whether both dilutions fall within the calibration curve (concentration / dilution)
If so, check which dilution has the lowest RSD
If both RSD are low, report the mean

Save ICP-MS data in wide format

Add Gibbs plot

Check Tamburello et al. 2022

Add calculation of ion balance for IC data

Check correct Piper plot compared to major cations plot

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