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plot_ena_summaries.R
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plot_ena_summaries.R
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# plot ENA metadata status
plot_ena_summaries <- function(
dat_all,
dat_mixs,
col,
ymax_all = 180000,
ymax_mixs = 80000
) {
# format x axis
bp <- barplot(
as.matrix(
data.frame(dat_all[, -1], check.names = F)
),
plot = F
)
# plot 1: complete data set
plot(
0, 0,
type = "n",
axes = F,
xlim = c(min(bp), max(bp)),
ylim = c(0, ymax_all),
lwd = 0.5
)
axis(
2,
at = seq(0, ymax_all, 20000),
las = 2,
cex.axis = 1.3,
mgp = c(2.5, 0.5, 0),
tcl = -0.3,
lwd = 0.5
)
# abline(h = ymax_mixs)
barplot(
as.matrix(
data.frame(dat_all[, -1], check.names = F)
),
col = col,
legend.text = dat_all[, 1],
args.legend = list(
x = "topleft",
bty = "n",
# legend = rev(paste0(dat_all[, 1], " (", round(rowSums(dat_all[, -1])/sum(dat_all[, -1]) * 100), "%)")),
cex = 1.3
),
names.arg = rep("", length(bp)),
add = T,
axes = F,
lwd = 0.5
)
par(xpd = NA)
tmp_prop <- prop.table(
as.matrix(
data.frame(dat_all[, -1], check.names = F)
),
2
) * 100
tmp_prop <- tmp_prop[nrow(tmp_prop):1, ]
text(
rep(bp, each = nrow(dat_all)),
rep(line2user(seq(0, 2.5, length.out = nrow(dat_all)), side = 1), length(bp)),
# pos = 1,
labels = ifelse(is.na(tmp_prop), "", round(tmp_prop)),
cex = 0.8
)
text(
rep(line2user(0, side = 2), nrow(dat_all)),
line2user(seq(0, 2.5, length.out = nrow(dat_all)), side = 1),
# pos = 1,
labels = rev(dat_all[, 1]),
adj = 1,
cex = 0.8
)
par(xpd = F)
axis(1, at = bp, col = NA, col.ticks = NA, labels = colnames(dat_all)[-1], las = 2, mgp = c(3, 3, 0), hadj = 1, cex.axis = 1.3)
# plot 2: MIxS checklists used
plot(
0, 0,
type = "n",
axes = F,
xlim = c(min(bp), max(bp)),
ylim = c(0, ymax_mixs),
lwd = 0.5
)
axis(
2,
at = seq(0, ymax_mixs, 10000),
las = 2,
cex.axis = 1.3,
mgp = c(2.5, 0.5, 0),
tcl = -0.3,
lwd = 0.5
)
barplot(
as.matrix(
data.frame(dat_mixs[, -1], check.names = F)
),
ylim = c(0, ymax_mixs),
names.arg = rep("", length(bp)),
col = col,
add = T,
axes = F,
lwd = 0.5
# legend.text = dat_mixs[, 1],
# args.legend = list(
# x = "topleft",
# # legend = rev(paste0(dat_mixs[, 1], " (", round(rowSums(dat_mixs[, -1])/sum(dat_mixs[, -1]) * 100), "%)"))
# bty = "n",
# cex = 1.3
# )
)
par(xpd = NA)
tmp_prop <- prop.table(
as.matrix(
data.frame(dat_mixs[, -1], check.names = F)
),
2
) * 100
tmp_prop <- tmp_prop[nrow(tmp_prop):1, ]
text(
rep(bp, each = nrow(dat_mixs)),
rep(line2user(seq(0, 2.5, length.out = nrow(dat_mixs)), side = 1), length(bp)),
# pos = 1,
labels = ifelse(is.na(tmp_prop), "", round(tmp_prop)),
cex = 0.8
)
# text(
# rep(line2user(0, side = 2), nrow(dat_mixs)),
# line2user(seq(0, 2.5, length.out = nrow(dat_mixs)), side = 1),
# # pos = 1,
# labels = rev(dat_mixs[, 1]),
# adj = 1,
# cex = 0.8
# )
par(xpd = F)
axis(1, at = bp, col = NA, col.ticks = NA, labels = colnames(dat_mixs)[-1], las = 2, mgp = c(3, 3, 0), hadj = 1, cex.axis = 1.3)
}