fix global variable binding

ManonMartin · Mar 19, 2024 · e967f2a · e967f2a
1 parent 25426d3
commit e967f2a
Show file tree

Hide file tree

Showing 3 changed files with 19 additions and 17 deletions.
diff --git a/R/lmpContributions.R b/R/lmpContributions.R
@@ -129,13 +129,13 @@ lmpContributions <- function(resLmpPcaEffects, nPC = 5) {
         varPercentage = unname(resLmpPcaEffects$variationPercentages)
     )
 
-    plotTotal <- ggplot2::ggplot(
+    plotTotal <- with(dataTotal,{ggplot2::ggplot(
         data = dataTotal,
         ggplot2::aes(
             x = stats::reorder(effects, -varPercentage),
             y = varPercentage
         )
-    ) +
+    )}) +
         ggplot2::geom_bar(stat = "identity") +
         ggplot2::xlab("Effects") +
         ggplot2::ylab("Percentage of Variance") +
@@ -157,7 +157,7 @@ lmpContributions <- function(resLmpPcaEffects, nPC = 5) {
 
     dataContrib <- as.data.frame(effect_vector[seq_len(10)])
 
-    plotContrib <- ggplot2::ggplot(
+    plotContrib <- with(dataContrib, {ggplot2::ggplot(
         data = dataContrib,
         ggplot2::aes(
             x = stats::reorder(
@@ -166,11 +166,11 @@ lmpContributions <- function(resLmpPcaEffects, nPC = 5) {
             ),
             y = dataContrib[, 1]
         )
-    ) +
+    )}) +
         ggplot2::geom_bar(stat = "identity") +
         ggplot2::xlab("Contributions") +
         ggplot2::ylab("Percentage of Variance") +
-        ggplot2::scale_x_discrete(limits = rownames(data)) +
+        ggplot2::scale_x_discrete(limits = rownames(dataContrib)) +
         ggplot2::theme_bw()
 
 

diff --git a/R/pcaScreePlot.R b/R/pcaScreePlot.R
@@ -38,7 +38,7 @@ pcaScreePlot <- function(resPcaBySvd, nPC = 5,
     res <- data.frame(var = resPcaBySvd$var[seq_len(nPC)])
     res <- res %>% rownames_to_column("PC")
 
-    ggplot2::ggplot(
+    with(res, {ggplot2::ggplot(
         data = res,
         ggplot2::aes(
             x = factor(PC, levels = PC),
@@ -49,5 +49,5 @@ pcaScreePlot <- function(resPcaBySvd, nPC = 5,
         ggplot2::xlab("Principal Components") +
         ggplot2::ylab("Percentage of Variance") +
         ggplot2::ggtitle(title) +
-        theme
+        theme})
 }
diff --git a/R/plotLine.R b/R/plotLine.R
@@ -127,31 +127,31 @@ plotLine <- function(Y, rows = 1, type = c("l", "p", "s"),
 
     if (!is.null(color)) {
         if (color == "rows") {
-            fig <- ggplot2::ggplot(
+            fig <- with(Y_long, {ggplot2::ggplot(
                 data = Y_long,
                 ggplot2::aes(
                     x = x_axis, y = value,
                     group = rownames, color = rownames
                 )
-            )
+            )})
             color <- NULL
         } else {
-            fig <- ggplot2::ggplot(
+            fig <- with(Y_long, {ggplot2::ggplot(
                 data = Y_long,
                 ggplot2::aes(
                     x = x_axis, y = value,
                     group = rownames
                 )
-            )
+            )})
         }
     } else {
-        fig <- ggplot2::ggplot(
+        fig <- with(Y_long, {ggplot2::ggplot(
             data = Y_long,
             ggplot2::aes(
                 x = x_axis, y = value,
                 group = rownames
             )
-        )
+        )})
     }
 
 
@@ -203,13 +203,15 @@ plotLine <- function(Y, rows = 1, type = c("l", "p", "s"),
 
     if (type == "s") {
         if (!is.null(color)) {
-            fig <- fig + ggplot2::geom_segment(aes(xend = x_axis, yend = 0),
+            fig <- with(Y_long,{fig +
+                ggplot2::geom_segment(aes(xend = x_axis, yend = 0),
                 size = size, lineend = "round", color = color
-            )
+            )})
         } else {
-            fig <- fig + ggplot2::geom_segment(aes(xend = x_axis, yend = 0),
+            fig <- with(Y_long,{fig +
+                ggplot2::geom_segment(aes(xend = x_axis, yend = 0),
                 size = size, lineend = "round"
-            )
+                )})
         }
     }