fix use of deprecated ggplot terms

- size replaced with linewidth for geom_line and element_line
- replace aes_ and aes_string with aes and use .data

R/glog_transformation.R

@@ -125,11 +125,12 @@ glog_plot_optimised_lambda <- function(df, optimised_lambda, classes, qc_label,
         length.out=plot_grid))
     sse_df$SSE <- vapply(X=sse_df$lambda, FUN=SSE, y0=0, y=assay(df_qc), 
         FUN.VALUE=numeric(1))
-    g <- ggplot(data=sse_df, aes_string(x='lambda',y='SSE')) +
+    g <- ggplot(data=sse_df, aes(x=data[['lambda']],y=data[['SSE']])) +
         geom_vline(xintercept=optimised_lambda, color="red") +
-        geom_line(size=1.1) + theme_bw() +
+        geom_line(linewidth=1.1) + theme_bw() +
         labs (title="glog parameter optimisation",
-            caption=paste("optimum = ",round(optimised_lambda,2), sep=""))
+            caption=paste("optimum = ",round(optimised_lambda,2), sep=""))+
+        xlab('lambda') + ylab('SSE')
     return (g)
 }
 

R/sbc_plot.R

@@ -43,13 +43,13 @@ sbc_plot <- function(df, corrected_df, classes, batch, indexes = NULL,
     manual_color <- c("#386cb0", "#ef3b2c", "#7fc97f", "#fdb462", "#984ea3", 
         "#a6cee3", "#778899", "#fb9a99", "#ffff33")
     gg_THEME <- theme(panel.background = element_blank(), 
-        panel.grid.major = element_line(color = "gray80", size = 0.3), 
+        panel.grid.major = element_line(color = "gray80", linewidth = 0.3), 
         axis.line = element_line(color = "black"), 
         axis.text = element_text(color = "black"), 
         axis.title = element_text(color = "black"), 
         panel.grid.minor.x = element_line(color = "gray80", 
-        size = 0.3, linetype = "dashed"), 
-        panel.grid.minor.y = element_line(color = "gray80", size = 0.3))
+            linewidth = 0.3, linetype = "dashed"), 
+        panel.grid.minor.y = element_line(color = "gray80", linewidth = 0.3))
     plots <- list()
     if (is.null(indexes) & nrow(df) >= 100) {
         indexes <- seq_len(100)
@@ -64,7 +64,10 @@ sbc_plot <- function(df, corrected_df, classes, batch, indexes = NULL,
         A <- melt(A, id.vars = c("x", "batch", "shapes"))
 
         plots[[peakn]] <- ggplot(A, 
-            aes_(~x, ~value, col = ~batch, shape = ~shapes)) + 
+            aes(x = .data[['x']], 
+                y = .data[['value']], 
+                col = .data[['batch']], 
+                shape = .data[['shapes']])) + 
             facet_grid(variable ~ .) + geom_point() + 
             scale_shape_identity() + geom_point(size=2) +
             scale_colour_manual(values = manual_color) +