Cyanobacteria-functional-ecology

The code aims at reproducing the analyses and figures presented in the paper titled Functional response of cyanobacteria to environmental changes. These code use the dataset located at: doi.org/10.34894/9X9YMO. The code uses R version 4.3.1.

Content

1. License
2. README
3. R scripts:

• Packages loading.R
• Material and Methods.R
• Results_Flow cytometry traits.R
• Results_Functional analyses from individual level.R
• Results_Functional assessment of natural communities.R

Reproduction of analyses and figures

Packages loading

Packages loading.R

Material and Methods

Material and Methods.R

The script details methodological steps necessar to prepare the data. The script produce figure 1 panels B to F.

Dataset: IndTraits

Results

Results_Flow cytometry traits.R

The script produces the figure 2.

Dataset: IndTraits

Results_Functional analyses from individual level.R

The script produces the figures 3 and 4. From Line 175 the code runs only for one treatment.

Dataset: IndTraits

Results_Functional assessment of natural communities.R

The script produces the figure 5. Ensure that you read the data set "DATA" to produce the functional fingerprints.

Datasets: IndTraits, CommTraits

List of packages and versions

# ==== Required Packages and Versions ====

# ggConvexHull      0.1.0
# svMisc            1.2.3
# dplyr             1.1.3
# ggplot2           3.5.1
# RColorBrewer      1.1-3
# ggrepel           0.9.4
# devtools          2.4.5
# PCAtest           0.0.1
# tidyr             1.3.0
# ggsci             3.0.0
# tictoc            1.2
# BAT               2.9.6
# reshape2          1.4.4
# ggpubr            0.6.0
# pheatmap          1.0.12
# hypervolume       3.1.3
# alphahull         2.5
# ade4              1.7-22
# ggExtra           0.10.1
# corrplot          0.92
# tidyverse         2.0.0
# ggnewscale        0.4.10
# ggpmisc           0.5.4-1
# scales            1.3.0
# cowplot           1.1.3