Merge pull request #34 from HendrikSchultheis/master

Export create_x plotting functions

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: wilson
 Type: Package
 Title: Web-Based Interactive Omics Visualization
-Version: 2.1.1
+Version: 2.2.0
 Authors@R: c(
     person("Hendrik", "Schultheis", email = "hendrik.schultheis@mpi-bn.mpg.de", role = c("aut", "cre")),
     person("Jens", "Preussner", email = "jens.preussner@mpi-bn.mpg.de", role = "aut"),

NAMESPACE

@@ -7,6 +7,10 @@ export(colorPicker)
 export(colorPickerUI)
 export(columnSelector)
 export(columnSelectorUI)
+export(create_geneview)
+export(create_heatmap)
+export(create_pca)
+export(create_scatterplot)
 export(featureSelector)
 export(featureSelectorUI)
 export(geneView)

NEWS.md

@@ -1,3 +1,5 @@
+# wilson 2.2.0
+- export plotting functions
 # wilson 2.1.1
 - fixed multiple unique_id bug in tobias_parser
 # wilson 2.1.0

R/function.R

@@ -33,6 +33,8 @@
 #' @import data.table
 #'
 #' @return Returns list(plot = ggplotly/ ggplot, width, height, ppi, exceed_size).
+#'
+#' @export
 create_scatterplot <- function(data, data.labels = NULL, data.hovertext = NULL, transparency = 1, pointsize = 1, labelsize = 3, color = NULL, x_label = "", y_label = "", z_label = "", density = TRUE, line = TRUE, categorized = FALSE, highlight.data = NULL, highlight.labels = NULL, highlight.hovertext = NULL, highlight.color = "#FF0000", xlim = NULL, ylim = NULL, colorbar.limits = NULL, width = "auto", height = "auto", ppi = 72, plot.method = "static", scale = 1){
   # force evaluation of all arguments
   # no promises in plot object
@@ -322,6 +324,8 @@ create_scatterplot <- function(data, data.labels = NULL, data.hovertext = NULL,
 #' @import data.table
 #'
 #' @return A named list(plot = ggplot object, data = pca.data, width = width of plot (cm), height = height of plot (cm), ppi = pixel per inch, exceed_size = Boolean whether width/ height exceeded max).
+#'
+#' @export
 create_pca <- function(data, color.group = NULL, color.title = NULL, palette = NULL, shape.group = NULL, shape.title = NULL, shapes = c(15:25), dimension.a = 1, dimension.b = 2, dimensions = 6, on.columns = TRUE, labels = FALSE, custom.labels = NULL, pointsize = 2, labelsize = 3, width = 28, height = 28, ppi = 72, scale = 1) {
   # force evaluation of all arguments
   # no promises in plot object
@@ -500,6 +504,8 @@ create_pca <- function(data, color.group = NULL, color.title = NULL, palette = N
 #' @details Width/ height limit = 500. If exceeded default to 500 and issue exceed_size = TRUE.
 #'
 #' @return Returns list(plot = complexHeatmap/ plotly object, width = width in cm, height = height in cm, ppi = pixel per inch, exceed_size = Boolean whether width/ height exceeded max) depending on plot.method.
+#'
+#' @export
 create_heatmap <- function(data, unitlabel = "auto", row.label = TRUE, row.custom.label = NULL, column.label = TRUE, column.custom.label = NULL, clustering = "none", clustdist = "auto", clustmethod = "auto", colors = NULL, winsorize.colors = NULL, plot.method = "static", width = "auto", height = "auto", ppi = 72, scale = 1) {
   # force evaluation of all arguments
   # no promises in plot object
@@ -771,6 +777,8 @@ create_heatmap <- function(data, unitlabel = "auto", row.label = TRUE, row.custo
 #' @import data.table
 #'
 #' @return Returns depending on plot.method list(plot = ggplot/ plotly object, width = width in cm, height = height in cm, ppi = pixel per inch, exceed_size = Boolean).
+#'
+#' @export
 create_geneview <- function(data, grouping, plot.type = "line", facet.target = "gene", facet.cols = 2, colors = NULL, ylabel = NULL, ylimits = NULL, gene.label = NULL, plot.method = "static", width = "auto", height = "auto", ppi = 72, scale = 1){
   # force evaluation of all arguments
   # no promises in plot object