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FIx for .data
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@Krgaric
Krgaric committed Oct 3, 2023
1 parent f8f18a0 commit 37dbb41
Showing 1 changed file with 30 additions and 30 deletions.
60 changes: 30 additions & 30 deletions rDNA/rDNA/R/rDNA.R
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Original file line number Diff line number Diff line change
Expand Up @@ -2221,52 +2221,52 @@ autoplot.dna_barplot <- function(object,

# Plot
g <- ggplot2::ggplot(object2,
ggplot2::aes(x = rlang::.data[["entity"]],
y = rlang::.data[["frequency"]],
fill = rlang::.data[["agreement"]],
group = rlang::.data[["agreement"]],
label = rlang::.data[["label"]]))
ggplot2::aes(x = .data[["entity"]],
y = .data[["frequency"]],
fill = .data[["agreement"]],
group = .data[["agreement"]],
label = .data[["label"]]))
if (binary) { # Bars for the binary case
g <- g + ggplot2::geom_bar(ggplot2::aes(fill = rlang::.data[["color"]],
color = rlang::.data[["text_color"]]),
stat = rlang::.data[["identity"]],
g <- g + ggplot2::geom_bar(ggplot2::aes(fill = .data[["color"]],
color = .data[["text_color"]]),
stat = .data[["identity"]],
width = barWidth,
show.legend = FALSE)
# For the integer case with positive and negative values
} else if (max(w) > 0 & min(w) < 0) {
g <- g + ggplot2::geom_bar(ggplot2::aes(fill = rlang::.data[["color"]],
color = rlang::.data[["text_color"]]),
g <- g + ggplot2::geom_bar(ggplot2::aes(fill = .data[["color"]],
color = .data[["text_color"]]),
stat = "identity",
width = barWidth,
show.legend = FALSE,
data = object2[as.numeric(as.character(object2$agreement)) >= 0, ],
position = ggplot2::position_stack(reverse = TRUE)) +
ggplot2::geom_bar(ggplot2::aes(fill = rlang::.data[["color"]],
color = rlang::.data[["text_color"]]),
ggplot2::geom_bar(ggplot2::aes(fill = .data[["color"]],
color = .data[["text_color"]]),
stat = "identity",
width = barWidth,
show.legend = FALSE,
data = object2[as.numeric(as.character(object2$agreement)) < 0, ])
# For the integer case with positive values only
} else if (min(w) >= 0) {
g <- g + ggplot2::geom_bar(ggplot2::aes(fill = rlang::.data[["color"]],
color = rlang::.data[["text_color"]]),
g <- g + ggplot2::geom_bar(ggplot2::aes(fill = .data[["color"]],
color = .data[["text_color"]]),
stat = "identity",
width = barWidth,
show.legend = FALSE,
position = ggplot2::position_stack(reverse = TRUE))
# For the integer case with negative values only
} else {
g <- g + ggplot2::geom_bar(ggplot2::aes(fill = rlang::.data[["color"]],
color = rlang::.data[["text_color"]]),
g <- g + ggplot2::geom_bar(ggplot2::aes(fill = .data[["color"]],
color = .data[["text_color"]]),
stat = "identity",
width = barWidth,
show.legend = FALSE)
}
g <- g + ggplot2::coord_flip() +
ggplot2::theme_minimal() +
# Add intercept line
ggplot2::geom_line(ggplot2::aes(x = rlang::.data[["x"]], y = rlang::.data[["y"]]),
ggplot2::geom_line(ggplot2::aes(x = .data[["x"]], y = .data[["y"]]),
data = yintercepts,
linewidth = axisWidth,
inherit.aes = FALSE) +
Expand All @@ -2283,35 +2283,35 @@ autoplot.dna_barplot <- function(object,
}
if (binary) { # Add entity labels for binary case
g <- g +
ggplot2::geom_text(ggplot2::aes(x = rlang::.data[["entity"]],
y = rlang::.data[["pos"]],
label = rlang::.data[["label"]]),
ggplot2::geom_text(ggplot2::aes(x = .data[["entity"]],
y = .data[["pos"]],
label = .data[["label"]]),
size = (fontSize / ggplot2::.pt),
inherit.aes = FALSE,
data = object2)
# Add entity labels for integer case with positive and negative values
} else if (max(w) > 0 & min(w) < 0) {
g <- g +
ggplot2::geom_text(ggplot2::aes(color = rlang::.data[["text_color"]]),
ggplot2::geom_text(ggplot2::aes(color = .data[["text_color"]]),
size = (fontSize / ggplot2::.pt),
position = ggplot2::position_stack(vjust = 0.5, reverse = TRUE),
inherit.aes = TRUE,
data = object2[object2$frequency >= 0, ]) +
ggplot2::geom_text(ggplot2::aes(color = rlang::.data[["text_color"]]),
ggplot2::geom_text(ggplot2::aes(color = .data[["text_color"]]),
size = (fontSize / ggplot2::.pt),
position = ggplot2::position_stack(vjust = 0.5),
inherit.aes = TRUE,
data = object2[object2$frequency < 0, ])
# Add entity labels for integer case with positive values only
} else if (min(w) >= 0) {
g <- g +
ggplot2::geom_text(ggplot2::aes(color = rlang::.data[["text_color"]]),
ggplot2::geom_text(ggplot2::aes(color = .data[["text_color"]]),
size = (fontSize / ggplot2::.pt),
position = ggplot2::position_stack(vjust = 0.5, reverse = TRUE),
inherit.aes = TRUE)
} else {
g <- g +
ggplot2::geom_text(ggplot2::aes(color = rlang::.data[["text_color"]]),
ggplot2::geom_text(ggplot2::aes(color = .data[["text_color"]]),
size = (fontSize / ggplot2::.pt),
position = ggplot2::position_stack(vjust = 0.5),
inherit.aes = TRUE)
Expand Down Expand Up @@ -2848,10 +2848,10 @@ autoplot.dna_backbone <- function(object, ..., ma = 500) {
bd$accept_ratio <- stats::filter(bd$acceptance, rep(1 / ma, ma), sides = 1)

# temperature and acceptance probability
g_accept <- ggplot2::ggplot(bd, ggplot2::aes(y = rlang::.data[["temperature"]], x = rlang::.data[["iteration"]])) +
g_accept <- ggplot2::ggplot(bd, ggplot2::aes(y = .data[["temperature"]], x = .data[["iteration"]])) +
ggplot2::geom_line(color = "#a50f15") +
ggplot2::geom_line(data = bd[bd$acceptance_prob >= 0, ],
ggplot2::aes(y = rlang::.data[["acceptance_prob"]], x = rlang::.data[["iteration"]])) +
ggplot2::aes(y = .data[["acceptance_prob"]], x = .data[["iteration"]])) +
ggplot2::ylab("Acceptance probability") +
ggplot2::xlab("Iteration") +
ggplot2::ggtitle("Temperature and acceptance probability") +
Expand All @@ -2865,7 +2865,7 @@ autoplot.dna_backbone <- function(object, ..., ma = 500) {
yl <- "Backbone loss"
ti <- "Spectral backbone distance"
}
g_loss <- ggplot2::ggplot(bd, ggplot2::aes(y = rlang::.data[["bb_loss"]], x = rlang::.data[["iteration"]])) +
g_loss <- ggplot2::ggplot(bd, ggplot2::aes(y = .data[["bb_loss"]], x = .data[["iteration"]])) +
ggplot2::geom_line() +
ggplot2::ylab(yl) +
ggplot2::xlab("Iteration") +
Expand All @@ -2877,7 +2877,7 @@ autoplot.dna_backbone <- function(object, ..., ma = 500) {
size = c(bd$current_size_ma, bd$optimal_size_ma),
Criterion = c(rep("Current iteration", nrow(bd)),
rep("Best solution", nrow(bd))))
g_size <- ggplot2::ggplot(d, ggplot2::aes(y = rlang::.data[["size"]], x = rlang::.data[["iteration"]], color = rlang::.data[["Criterion"]])) +
g_size <- ggplot2::ggplot(d, ggplot2::aes(y = .data[["size"]], x = .data[["iteration"]], color = .data[["Criterion"]])) +
ggplot2::geom_line() +
ggplot2::ylab(paste0("Number of elements (MA, last ", ma, ")")) +
ggplot2::xlab("Iteration") +
Expand All @@ -2886,7 +2886,7 @@ autoplot.dna_backbone <- function(object, ..., ma = 500) {
ggplot2::theme(legend.position = "bottom")

# ratio of recent acceptances
g_ar <- ggplot2::ggplot(bd, ggplot2::aes(y = rlang::.data[["accept_ratio"]], x = rlang::.data[["iteration"]])) +
g_ar <- ggplot2::ggplot(bd, ggplot2::aes(y = .data[["accept_ratio"]], x = .data[["iteration"]])) +
ggplot2::geom_line() +
ggplot2::ylab(paste("Acceptance ratio in the last", ma, "iterations")) +
ggplot2::xlab("Iteration") +
Expand Down Expand Up @@ -2937,7 +2937,7 @@ autoplot.dna_backbone <- function(object, ..., ma = 500) {
circular = FALSE,
height = height) + # TODO @Tim: "height" does not seem to exist
ggraph::geom_edge_elbow() +
ggraph::geom_node_point(aes(filter = rlang::.data[["leaf"]])) +
ggraph::geom_node_point(aes(filter = .data[["leaf"]])) +
ggplot2::theme_bw() +
ggplot2::theme(panel.border = element_blank(),
axis.title = element_blank(),
Expand Down

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