1. singleCellTK
  2. Commit b2b63db0164d7036faa4367297a8ed1435e84fcd
Browse code

color of scatterplot adjustable with colorLow, etc. arguments

Yusuke Koga authored on 22/06/2020 16:34:02
Showing 6 changed files
R/doubletFinder_doubletDetection.R
History View file @ b2b63db0
... ... 
@@ -156,7 +156,9 @@ runDoubletFinder <- function(inSCE,
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       ))
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       result <- suppressMessages(Seurat::RunUMAP(result,
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                                                  dims = 1:10,
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-                                                 verbose = verbose))
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+                                                 verbose = verbose,
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+                                                 umap.method = "umap-learn",
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+                                                 metric = "correlation"))
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       seuratDims <- Seurat::Embeddings(result, reduction = "umap")
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       umapDims[sceSampleInd, 1] <- seuratDims[,1]
R/ggPlotting.R
History View file @ b2b63db0
... ... 
@@ -25,6 +25,15 @@
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 #'  Default NULL.
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 #' @param dotSize Size of dots. Default 2.
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 #' @param transparency Transparency of the dots, values will be 0-1. Default 1.
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+#' @param colorLow Character. A color available from `colors()`.
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+#'  The color will be used to signify the lowest values on the scale.
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+#'  Default 'white'.
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+#' @param colorMid Character. A color available from `colors()`.
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+#'  The color will be used to signify the midpoint on the scale.
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+#'  Default 'gray'.
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+#' @param colorHigh Character. A color available from `colors()`.
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+#'  The color will be used to signify the highest values on the scale.
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+#'  Default 'blue'.
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 #' @param defaultTheme Removes grid in plot and sets axis title size to 10
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 #'  when TRUE. Default TRUE.
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 #' @param title Title of plot. Default NULL.
... ... 
@@ -48,6 +57,9 @@
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                        binLabel = NULL,
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                        dotSize = 2,
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                        transparency = 1,
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+                       colorLow = "white",
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+                       colorMid = "gray",
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+                       colorHigh = "blue",
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                        defaultTheme = TRUE,
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                        title = NULL,
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                        titleSize = 15,
... ... 
@@ -137,6 +149,14 @@
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     if (!is.null(colorBySub)) {
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       g <- g + ggplot2::aes_string(color = "color")
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     }
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+    if (class(colorBySub) == "numeric"){
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+        g <- g + ggplot2::scale_color_gradient2(
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+            low = colorLow,
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+            mid = colorMid,
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+            high = colorHigh,
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+            aesthetics = "colour",
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+            midpoint = mean(colorBySub))
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+    }
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     if (!is.null(shape)) {
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       g <- g + ggplot2::aes_string(shape = "shape") +
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         ggplot2::labs(shape = shape)
... ... 
@@ -227,6 +247,15 @@
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 #'  Default NULL.
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 #' @param dotSize Size of dots. Default 2.
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 #' @param transparency Transparency of the dots, values will be 0-1. Default 1.
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+#' @param colorLow Character. A color available from `colors()`.
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+#'  The color will be used to signify the lowest values on the scale.
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+#'  Default 'white'.
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+#' @param colorMid Character. A color available from `colors()`.
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+#'  The color will be used to signify the midpoint on the scale.
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+#'  Default 'gray'.
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+#' @param colorHigh Character. A color available from `colors()`.
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+#'  The color will be used to signify the highest values on the scale.
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+#'  Default 'blue'.
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 #' @param defaultTheme adds grid to plot when TRUE. Default TRUE.
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 #' @param title Title of plot. Default NULL.
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 #' @param titleSize Size of title of plot. Default 15.
... ... 
@@ -263,6 +292,9 @@ plotSCEDimReduceColData <- function(inSCE,
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                                     binLabel = NULL,
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                                     dotSize = 2,
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                                     transparency = 1,
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+                                    colorLow = "white",
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+                                    colorMid = "gray",
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+                                    colorHigh = "blue",
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                                     defaultTheme = TRUE,
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                                     title = NULL,
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                                     titleSize = 15,
... ... 
@@ -285,6 +317,9 @@ plotSCEDimReduceColData <- function(inSCE,
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     binLabel = binLabel,
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     dotSize = dotSize,
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     transparency = transparency,
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+    colorLow = colorLow,
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+    colorMid = colorMid,
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+    colorHigh = colorHigh,
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     defaultTheme = defaultTheme,
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     title = title,
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     titleSize = titleSize,
... ... 
@@ -321,6 +356,15 @@ plotSCEDimReduceColData <- function(inSCE,
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 #'  Default NULL.
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 #' @param dotSize Size of dots. Default 2.
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 #' @param transparency Transparency of the dots, values will be 0-1. Default 1.
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+#' @param colorLow Character. A color available from `colors()`.
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+#'  The color will be used to signify the lowest values on the scale.
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+#'  Default 'white'.
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+#' @param colorMid Character. A color available from `colors()`.
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+#'  The color will be used to signify the midpoint on the scale.
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+#'  Default 'gray'.
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+#' @param colorHigh Character. A color available from `colors()`.
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+#'  The color will be used to signify the highest values on the scale.
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+#'  Default 'blue'.
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 #' @param defaultTheme adds grid to plot when TRUE. Default TRUE.
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 #' @param title Title of plot. Default NULL.
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 #' @param titleSize Size of title of plot. Default 15.
... ... 
@@ -347,6 +391,9 @@ plotSCEDimReduceFeatures <- function(inSCE,
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                                      binLabel = NULL,
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                                      dotSize = 2,
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                                      transparency = 1,
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+                                     colorLow = "white",
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+                                     colorMid = "gray",
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+                                     colorHigh = "blue",
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                                      defaultTheme = TRUE,
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                                      title = NULL,
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                                      titleSize = 15,
... ... 
@@ -366,6 +413,9 @@ plotSCEDimReduceFeatures <- function(inSCE,
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     colorBy = counts,
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     shape = shape,
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     transparency = 1,
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+    colorLow = colorLow,
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+    colorMid = colorMid,
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+    colorHigh = colorHigh,
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     reducedDimName = reducedDimName,
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     xlab = xlab,
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     ylab = ylab,
... ... 
@@ -416,6 +466,15 @@ plotSCEDimReduceFeatures <- function(inSCE,
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 #'  Default NULL.
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 #' @param dotSize Size of dots. Default 2.
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 #' @param transparency Transparency of the dots, values will be 0-1. Default 1.
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+#' @param colorLow Character. A color available from `colors()`.
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+#'  The color will be used to signify the lowest values on the scale.
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+#'  Default 'white'.
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+#' @param colorMid Character. A color available from `colors()`.
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+#'  The color will be used to signify the midpoint on the scale.
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+#'  Default 'gray'.
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+#' @param colorHigh Character. A color available from `colors()`.
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+#'  The color will be used to signify the highest values on the scale.
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+#'  Default 'blue'.
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 #' @param defaultTheme adds grid to plot when TRUE. Default TRUE.
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 #' @param title Title of plot. Default NULL.
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 #' @param titleSize Size of title of plot. Default 15.
... ... 
@@ -445,6 +504,9 @@ plotSCEScatter <- function(inSCE,
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                            binLabel = NULL,
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                            dotSize = 2,
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                            transparency = 1,
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+                           colorLow = "white",
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+                           colorMid = "gray",
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+                           colorHigh = "blue",
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                            defaultTheme = TRUE,
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                            title = NULL,
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                            titleSize = 15,
... ... 
@@ -491,6 +553,9 @@ plotSCEScatter <- function(inSCE,
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     binLabel = binLabel,
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     dotSize = dotSize,
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     transparency = transparency,
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+    colorLow = colorLow,
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+    colorMid = colorMid,
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+    colorHigh = colorHigh,
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     defaultTheme = defaultTheme,
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     title = title,
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     titleSize = titleSize,
man/dot-ggScatter.Rd
History View file @ b2b63db0
... ... 
@@ -20,6 +20,9 @@
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   binLabel = NULL,
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   dotSize = 2,
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   transparency = 1,
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+  colorLow = "white",
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+  colorMid = "gray",
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+  colorHigh = "blue",
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   defaultTheme = TRUE,
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   title = NULL,
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   titleSize = 15,
... ... 
@@ -68,6 +71,18 @@ Default NULL.}
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 \item{transparency}{Transparency of the dots, values will be 0-1. Default 1.}
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+\item{colorLow}{Character. A color available from `colors()`.
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+The color will be used to signify the lowest values on the scale.
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+Default 'white'.}
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+
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+\item{colorMid}{Character. A color available from `colors()`.
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+The color will be used to signify the midpoint on the scale.
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+Default 'gray'.}
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+
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+\item{colorHigh}{Character. A color available from `colors()`.
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+The color will be used to signify the highest values on the scale.
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+Default 'blue'.}
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+
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 \item{defaultTheme}{Removes grid in plot and sets axis title size to 10
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 when TRUE. Default TRUE.}
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man/plotSCEDimReduceColData.Rd
History View file @ b2b63db0
... ... 
@@ -19,6 +19,9 @@ plotSCEDimReduceColData(
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   binLabel = NULL,
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   dotSize = 2,
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   transparency = 1,
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+  colorLow = "white",
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+  colorMid = "gray",
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+  colorHigh = "blue",
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   defaultTheme = TRUE,
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   title = NULL,
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   titleSize = 15,
... ... 
@@ -66,6 +69,18 @@ Default NULL.}
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 \item{transparency}{Transparency of the dots, values will be 0-1. Default 1.}
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+\item{colorLow}{Character. A color available from `colors()`.
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+The color will be used to signify the lowest values on the scale.
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+Default 'white'.}
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+
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+\item{colorMid}{Character. A color available from `colors()`.
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+The color will be used to signify the midpoint on the scale.
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+Default 'gray'.}
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+
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+\item{colorHigh}{Character. A color available from `colors()`.
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+The color will be used to signify the highest values on the scale.
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+Default 'blue'.}
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+
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 \item{defaultTheme}{adds grid to plot when TRUE. Default TRUE.}
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 \item{title}{Title of plot. Default NULL.}
man/plotSCEDimReduceFeatures.Rd
History View file @ b2b63db0
... ... 
@@ -19,6 +19,9 @@ plotSCEDimReduceFeatures(
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   binLabel = NULL,
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   dotSize = 2,
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   transparency = 1,
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+  colorLow = "white",
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+  colorMid = "gray",
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+  colorHigh = "blue",
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   defaultTheme = TRUE,
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   title = NULL,
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   titleSize = 15,
... ... 
@@ -64,6 +67,18 @@ Default NULL.}
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 \item{transparency}{Transparency of the dots, values will be 0-1. Default 1.}
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+\item{colorLow}{Character. A color available from `colors()`.
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+The color will be used to signify the lowest values on the scale.
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+Default 'white'.}
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+
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+\item{colorMid}{Character. A color available from `colors()`.
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+The color will be used to signify the midpoint on the scale.
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+Default 'gray'.}
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+
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+\item{colorHigh}{Character. A color available from `colors()`.
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+The color will be used to signify the highest values on the scale.
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+Default 'blue'.}
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+
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 \item{defaultTheme}{adds grid to plot when TRUE. Default TRUE.}
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 \item{title}{Title of plot. Default NULL.}
man/plotSCEScatter.Rd
History View file @ b2b63db0
... ... 
@@ -21,6 +21,9 @@ plotSCEScatter(
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   binLabel = NULL,
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   dotSize = 2,
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   transparency = 1,
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+  colorLow = "white",
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+  colorMid = "gray",
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+  colorHigh = "blue",
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   defaultTheme = TRUE,
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   title = NULL,
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   titleSize = 15,
... ... 
@@ -74,6 +77,18 @@ Default NULL.}
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 \item{transparency}{Transparency of the dots, values will be 0-1. Default 1.}
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+\item{colorLow}{Character. A color available from `colors()`.
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+The color will be used to signify the lowest values on the scale.
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+Default 'white'.}
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+
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+\item{colorMid}{Character. A color available from `colors()`.
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+The color will be used to signify the midpoint on the scale.
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+Default 'gray'.}
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+
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+\item{colorHigh}{Character. A color available from `colors()`.
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+The color will be used to signify the highest values on the scale.
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+Default 'blue'.}
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+
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 \item{defaultTheme}{adds grid to plot when TRUE. Default TRUE.}
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 \item{title}{Title of plot. Default NULL.}