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Order trait coverage labels in decreasing order #95

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merged 2 commits into from
Jan 12, 2024
Merged

Order trait coverage labels in decreasing order #95

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a84f368
Make sure coverages are in decreasing order within species category
Jan 12, 2024
267dbfb
Merge branch 'main' into fix_all_traits_position
Jan 12, 2024
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30 changes: 19 additions & 11 deletions R/fb_plot_site_traits_completeness.R
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Original file line number Diff line number Diff line change
Expand Up @@ -50,6 +50,8 @@ fb_plot_site_traits_completeness <- function(
function(x) site_species[, c("site", x), drop = FALSE]
)


# Compute site-level trait coverage for all traits
all_coverage <- lapply(
site_species_categories,
function(x) fb_get_all_trait_coverages_by_site(
Expand Down Expand Up @@ -98,10 +100,11 @@ fb_plot_site_traits_completeness <- function(
)


# Get average coverage
# Compute average trait coverage across all sites for each trait
avg_coverage <- lapply(
all_coverage,
function(x) {

avg_coverage <- by(
x, x$coverage_name,
function(y) mean(y$coverage_value, na.rm = TRUE)
Expand All @@ -118,13 +121,21 @@ fb_plot_site_traits_completeness <- function(
)
)

avg_coverage <- avg_coverage[, c("cov_label", "coverage_name")]
avg_coverage <- t(utils::unstack(avg_coverage))
# Re-order to make sure of coverage is decreasing
avg_coverage <- avg_coverage[
order(avg_coverage$avg_coverage, decreasing = TRUE),
]

# Transform into factor to keep order
avg_coverage$cov_label <- factor(
avg_coverage$cov_label, levels = avg_coverage$cov_label
)

return(avg_coverage)
}
)


# Add categories back into data.frame
# Add species categories back into final data.frame
all_coverage <- lapply(
names(all_coverage),
function(x) {
Expand All @@ -143,10 +154,7 @@ fb_plot_site_traits_completeness <- function(
names(avg_coverage),
function(x) {

given_coverage <- data.frame(
coverage_name = colnames(avg_coverage[[x]]),
avg_coverage = as.character(avg_coverage[[x]])
)
given_coverage <- avg_coverage[[x]]

given_coverage[category_name] <- x

Expand Down Expand Up @@ -183,8 +191,8 @@ fb_plot_site_traits_completeness <- function(
ggplot2::ggplot(
all_coverage,
ggplot2::aes(
interaction(.data$avg_coverage, .data[[category_name]], sep = "__"), .data$site,
fill = .data$coverage_value
interaction(.data$cov_label, .data[[category_name]], sep = "__"),
.data$site, fill = .data$coverage_value
)
) +
ggplot2::geom_tile() +
Expand Down
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