Extract soil P Retention Classes for Accessions in Root Phenotype Study

1 Loading Libraries

library(dplyr)
library(soilP)
library(ggplot2)

2 Loading stored data from previous workflow steps

data(soilclass)
data(ISRIC2011)
data_dir <- system.file("data", package = "soilP", mustWork = TRUE)
extdata_dir <- system.file("extdata", package = "soilP", mustWork = TRUE)

3 Importing maize accession collection coordinates

grin_file <- file.path(extdata_dir, "GRIN.csv")
grin <- read.csv(grin_file) %>%
        select(accenumb,longdec, latdec, elevation)

4 Importing Burton 2013 maize accession root phenotypes

burton_file <- file.path(extdata_dir,"burton2013.csv")
burton2013 <- read.csv(burton_file)

5 Merging georefence data and phenotype data

georef <- burton2013 %>%
          left_join(grin, by = c("Accession" = "accenumb"))

Column `Accession`/`accenumb` joining factors with different levels, coercing to character vector

# minor correction for an Argentinian Accession in GRIN
georef[georef$Accession == "PI 516074",
       c("longdec","latdec")] <- c(-68.064167, -38.9525)
georef$elevation.class <- classify_elevation(georef$elevation)

6 Obtainning P retention classes form coordinates

ISRIC_P <- extract_P_ISRIC(ISRIC2011, georef, soilclass,
                           lon = "longdec", lat = "latdec")

Joining, by = "ascending"

7 Plotting Phosphorus Retention Potential Maps

data(mountain)
bg_map("longdec", "latdec", data = ISRIC_P$georef, bg = mountain) +
  geom_point(aes(x = longdec, y = latdec,
                 shape = elevation.class,
                 colour = main), 
             data = ISRIC_P$georef) +
  facet_wrap( ~ domestication, ncol = 2) +
  scale_color_manual(values = ISRIC_P$pal,
                     name = "Phosphorus\nRetention\nPotential",
                     breaks = ISRIC_P$breaks ) +
  scale_shape_manual(values = c(16,15, 17, 18))