@@ -11,7 +11,7 @@ License: GPL (>= 3)

 Encoding: UTF-8

 LazyData: true

 Roxygen: list(markdown = TRUE)

-RoxygenNote: 7.1.1

+RoxygenNote: 7.1.2

 biocViews:

 Imports: 

     BiocGenerics,

@@ -6,6 +6,10 @@ S3method(cbind,poplin.matrix)

 S3method(poplin_biplot,default)

 S3method(poplin_biplot,poplin.pca)

 S3method(poplin_biplot,poplin.plsda)

+S3method(poplin_boxplot,default)

+S3method(poplin_boxplot,poplin)

+S3method(poplin_corplot,default)

+S3method(poplin_corplot,poplin)

 S3method(poplin_scoreplot,default)

 S3method(poplin_scoreplot,poplin.pca)

 S3method(poplin_scoreplot,poplin.plsda)

@@ -14,7 +18,6 @@ S3method(rbind,poplin.matrix)

 S3method(summary,poplin.pca)

 S3method(summary,poplin.plsda)

 S3method(summary,poplin.tsne)

-export("missingCount<-")

 export("poplinData<-")

 export("poplinReducedData<-")

 export("poplin_data<-")

@@ -41,13 +44,12 @@ export(.set_poplinReducedData_data_integer)

 export(.set_poplinReducedData_data_missing)

 export(.set_poplinReducedData_datalist)

 export(.verify_and_extract_input)

-export(missingCount)

-export(plot_box)

-export(plot_cor)

 export(poplin)

 export(poplinData)

 export(poplinReducedData)

 export(poplin_biplot)

+export(poplin_boxplot)

+export(poplin_corplot)

 export(poplin_data)

 export(poplin_data_list)

 export(poplin_data_names)

@@ -86,7 +88,6 @@ exportClasses(poplin)

 exportClasses(poplin.matrix)

 exportMethods("[")

 exportMethods("[<-")

-exportMethods("missingCount<-")

 exportMethods("poplinData<-")

 exportMethods("poplinReducedData<-")

 exportMethods("poplin_data<-")

@@ -96,7 +97,6 @@ exportMethods("poplin_reduced<-")

 exportMethods("poplin_reduced_list<-")

 exportMethods("poplin_reduced_names<-")

 exportMethods(coerce)

-exportMethods(missingCount)

 exportMethods(poplinData)

 exportMethods(poplinReducedData)

 exportMethods(poplin_data)

@@ -1,11 +1,11 @@

 ##' @importFrom ggplot2 geom_segment scale_x_continuous scale_y_continuous sec_axis

 ##' @export

-poplin_biplot <- function(x, comp = 1:2, ...) {

+poplin_biplot <- function(x, ...) {

   UseMethod("poplin_biplot")

 }

 ##' @export

-poplin_biplot.default <- function(x, y, comp, group,

+poplin_biplot.default <- function(x, y, comp = 1:2, group,

                                   group_col = NULL,

                                   point_size = 1.5,

                                   point_shape_by_group = FALSE,

@@ -71,7 +71,7 @@ poplin_biplot.poplin.pca <- function(x, scale = 1, comp = 1:2, ...) {

   comp <- sort(comp)

   n <- nrow(x)

   lam <- attr(x, "sdev")[comp] * sqrt(n)

-  if (scale < 0 || scale > 1) 

+  if (scale < 0 || scale > 1)

     warning("'scale' is outside [0, 1]")

   if (scale != 0)

     lam <- lam**scale

new file mode 100644

@@ -0,0 +1,45 @@

+##' @export

+poplin_boxplot <- function(x, ...) {

+  UseMethod("poplin_boxplot")

+}

+

+##' @export

+##' @importFrom stats reshape

+##' @importFrom ggplot2 geom_boxplot geom_violin

+poplin_boxplot.default <- function(x, group, log2 = FALSE, violin = FALSE,

+                           ylab = "Intensity") {

+  ## convert wide to long format to draw fig

+  if (log2) {

+    x <- log2(x)

+  }

+  dt <- as.data.frame(t(x))

+  cols <- names(dt)

+  dt$id <- rownames(dt)

+  if (!missing(group)) {

+    dt$group <- group

+  }

+  dd <- reshape(dt, varying = cols, timevar = "feature",

+                times = cols, v.names = "value",

+                direction = "long", sep = "")

+  if (missing(group)) {

+    p <- ggplot(dd, aes(x = id, y = value))

+  } else {

+    p <- ggplot(dd, aes(x = id, y = value, fill = group))

+  }

+  if (violin) {

+    p <- p + geom_violin()

+  } else {

+    p <- p + geom_boxplot()

+  }

+  p +

+    ylab(ylab) +

+    theme_bw() +

+    theme(legend.title = element_blank(),

+          axis.title.x = element_blank())

+}

+

+##' @export

+poplin_boxplot.poplin <- function(x, poplin_in, ...) {

+  m <- .verify_and_extract_input(x, poplin_in)

+  poplin_boxplot.default(m, ...)

+}

new file mode 100644

@@ -0,0 +1,23 @@

+##' @export

+poplin_corplot <- function(x, ...) {

+  UseMethod("poplin_corplot")

+}

+

+##' @export

+##' @importFrom heatmaply ggheatmap

+poplin_corplot.default <- function(x,

+                     use = c("everything", "all.obs", "complete.obs",

+                             "na.or.complete", "pairwise.complete.obs"),

+                     method = c("pearson", "kendall", "spearman"),

+                     showticklabels = c(TRUE, TRUE), ...) {

+  use <- match.arg(use)

+  method <- match.arg(method)

+  m <- cor(x, use = use, method = method)

+  ggheatmap(m, showticklabels = showticklabels, ...)

+}

+

+##' @export

+poplin_corplot.poplin <- function(x, poplin_in , ...) {

+  m <- .verify_and_extract_input(x, poplin_in)

+  poplin_corplot.default(m, ...)

+}

deleted file mode 100644

@@ -1,62 +0,0 @@

-##' @export

-##' @importFrom stats reshape

-##' @importFrom ggplot2 geom_boxplot geom_violin

-plot_box <- function(x, group, log2 = FALSE, violin = FALSE) {

-  ## convert wide to long format to draw fig

-  if (log2) {

-    x <- log2(x)

-  }

-  dt <- as.data.frame(t(x))

-  cols <- names(dt)

-  dt$id <- rownames(dt)

-  if (!missing(group)) {

-    dt$group <- group

-  }

-  dd <- reshape(dt, varying = cols, timevar = "feature",

-                  times = cols, v.names = "value", 

-                  direction = "long", sep = "")

-  if (missing(group)) {

-    p <- ggplot(dd, aes(x = id, y = value))

-  } else {

-    p <- ggplot(dd, aes(x = id, y = value, fill = group))

-  }

-  if (violin) {

-    p <- p + geom_violin()

-  } else {

-    p <- p + geom_boxplot()

-  }

-  p +

-    ylab("Intensity") +

-    theme_bw() +

-    theme(legend.title = element_blank(),

-          axis.title.x = element_blank())

-}

-

-##' @export

-##' @importFrom heatmaply ggheatmap is.na10 heatmaply

-## plot_na <- function(x, grid_gap = 1, colors = c("gray80", "gray20"),

-##                     showticklabels = c(TRUE, FALSE),

-##                     ...) {

-

-##   p <- heatmaply(is.na10(x), grid_gap = grid_gap, colors = colors,

-##                  showticklabels = showticklabels,

-##                  hide_colorbar = TRUE, return_ppxpy = TRUE, ...)

-##   browser()

-##   ## heatmaply:::arrange_plots(plots = p)

-##   ## temporary issue in arrange_plots

-##   .arrange_plots(plots = p, hide_colorbar = TRUE)

-## }

-

-##' @export

-plot_cor <- function(x,

-                     use = c("everything", "all.obs", "complete.obs",

-                             "na.or.complete", "pairwise.complete.obs"),

-                     method = c("pearson", "kendall", "spearman"),

-                     showticklabels = c(TRUE, TRUE), ...) {

-  use <- match.arg(use)

-  method <- match.arg(method)

-  m <- cor(x, use = use, method = method)

-  ggheatmap(m, showticklabels = showticklabels, ...)

-}

-

-