# Labels
labels = c(bacteria = "Bacteria",
fits1 = "Fungi (ITS1)",
fits2 = "Fungi (ITS2)",
oomycetes = "Oomycetes",
nematodes = "Nematodes")
signif.labs <- c("pval > 0.05", "pval <= 0.05")
names(signif.labs) <- c("p value > 0.05", "p value <= 0.05")
# Pivot table
all_taxa_data_long <- pivot_longer(all_taxa_data,
cols = c(ndvi,
Shannon),
names_to = "type",
values_to = "value")
# Add significance
all_taxa_data_temp <- all_taxa_data %>%
add_column("pval") %>%
mutate(pval = ifelse(Taxa == "nematodes" , 0.00496, NA)) %>%
mutate(pval = ifelse(Taxa == "fits1",0.6, pval)) %>%
mutate(pval = ifelse(Taxa == "fits2",0.6, pval)) %>%
mutate(pval = ifelse(Taxa == "bacteria",0.6, pval)) %>%
mutate(pval = ifelse(Taxa == "oomycetes",0.6, pval)) %>%
mutate(signif = ifelse(pval <= 0.05, "pval <= 0.05", "pval > 0.05"))
all_taxa_data <- all_taxa_data_temp
# Scatter plot by group
theme_set(theme_bw())
ndvi_shannon_all <- ggplot(all_taxa_data,
aes(x = ndvi,
y = Shannon,
color = Taxa,
shape = Taxa)) +
geom_point(alpha = 0.8, size = 3) +
geom_smooth(method = "glm", formula = y~x, se = F,
method.args = list(family = gaussian(link = 'log')),
aes(color = Taxa, linetype = signif)) +
scale_shape_discrete(name = "Taxa", labels = labels,
breaks = c("bacteria", "fits1", "fits2", "nematodes", "oomycetes")) +
scale_color_viridis(name = "Taxa",
labels = labels,
begin = 0,
end = 0.8,
breaks = c("bacteria", "fits1", "fits2", "nematodes", "oomycetes"),
discrete = TRUE) +
scale_linetype_discrete(name= 'Significance',
guide = 'none') +
#labels = names(signif.labs)) +
#scale_linetype_manual(name = "Taxa",
#breaks = c("bacteria", "fits1", "fits2", "nematodes", "oomycetes")) +
theme(plot.title = element_text(hjust = 0.5 #,size = 20
),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_blank(),
strip.background = element_blank()) +
#axis.text = element_text(size = 20),
#text = element_text(size = 24)
xlab("NDVI") +
ylab("Alpha diversity")
ndvi_shannon_all
save_plot(ndvi_shannon_all, plot_name = paste0("ndvi_shannon_all"),
plot_width=13, plot_height=18)
sessionInfo()
## R version 4.4.2 (2024-10-31)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.5 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
##
## locale:
## [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
## [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
## [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
## [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
##
## time zone: Europe/Oslo
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] viridis_0.6.5 viridisLite_0.4.2 lubridate_1.9.4 forcats_1.0.0
## [5] stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2 readr_2.1.5
## [9] tidyr_1.3.1 tibble_3.2.1 tidyverse_2.0.0 ggplot2_3.5.1
##
## loaded via a namespace (and not attached):
## [1] sass_0.4.9 generics_0.1.3 stringi_1.8.4 lattice_0.22-6
## [5] hms_1.1.3 digest_0.6.37 magrittr_2.0.3 evaluate_1.0.1
## [9] grid_4.4.2 timechange_0.3.0 fastmap_1.2.0 jsonlite_1.8.9
## [13] Matrix_1.7-1 gridExtra_2.3 mgcv_1.9-1 scales_1.3.0
## [17] textshaping_0.4.1 jquerylib_0.1.4 cli_3.6.3 rlang_1.1.4
## [21] munsell_0.5.1 splines_4.4.2 withr_3.0.2 cachem_1.1.0
## [25] yaml_2.3.10 tools_4.4.2 tzdb_0.4.0 colorspace_2.1-1
## [29] vctrs_0.6.5 R6_2.5.1 lifecycle_1.0.4 ragg_1.3.3
## [33] pkgconfig_2.0.3 pillar_1.10.0 bslib_0.8.0 gtable_0.3.6
## [37] glue_1.8.0 systemfonts_1.1.0 xfun_0.49 tidyselect_1.2.1
## [41] rstudioapi_0.17.1 knitr_1.49 farver_2.1.2 htmltools_0.5.8.1
## [45] nlme_3.1-166 rmarkdown_2.29 labeling_0.4.3 compiler_4.4.2