@@ -21,7 +21,7 @@ plotSCEDimReduceColData(

   dim2 = NULL,

   bin = NULL,

   binLabel = NULL,

-  dotSize = 0.5,

+  dotSize = 0.1,

   transparency = 1,

   colorScale = NULL,

   colorLow = "white",

@@ -86,7 +86,7 @@ If more than one value, will bin numeric values using values as a cut point.}

 \item{binLabel}{Character vector. Labels for the bins created by the `bin` parameter.

 Default NULL.}

-\item{dotSize}{Size of dots. Default 0.5.}

+\item{dotSize}{Size of dots. Default 0.1.}

 \item{transparency}{Transparency of the dots, values will be 0-1. Default 1.}

@@ -138,6 +138,7 @@ Plot results of reduced dimensions data and

  colors by annotation data stored in the colData slot.

 }

 \examples{

+data("mouseBrainSubsetSCE")

 plotSCEDimReduceColData(

   inSCE = mouseBrainSubsetSCE, colorBy = "tissue",

   shape = NULL, conditionClass = "factor",

@@ -21,7 +21,7 @@ plotSCEDimReduceColData(

   dim2 = NULL,

   bin = NULL,

   binLabel = NULL,

-  dotSize = 2,

+  dotSize = 0.5,

   transparency = 1,

   colorScale = NULL,

   colorLow = "white",

@@ -86,7 +86,7 @@ If more than one value, will bin numeric values using values as a cut point.}

 \item{binLabel}{Character vector. Labels for the bins created by the `bin` parameter.

 Default NULL.}

-\item{dotSize}{Size of dots. Default 2.}

+\item{dotSize}{Size of dots. Default 0.5.}

 \item{transparency}{Transparency of the dots, values will be 0-1. Default 1.}

@@ -64,9 +64,13 @@ original class. Default NULL.}

 \item{ylab}{Character vector. Label for y-axis. Default NULL.}

-\item{axisSize}{Size of x/y-axis ticks. Default 10.}

+\item{baseSize}{The base font size for all text. Default 12.

+Can be overwritten by titleSize, axisSize, and axisLabelSize,

+legendSize, legendTitleSize.}

-\item{axisLabelSize}{Size of x/y-axis labels. Default 10.}

+\item{axisSize}{Size of x/y-axis ticks. Default NULL.}

+

+\item{axisLabelSize}{Size of x/y-axis labels. Default NULL.}

 \item{dim1}{1st dimension to be used for plotting. Can either be a string which specifies

 the name of the dimension to be plotted from reducedDims, or a numeric value which specifies

@@ -117,7 +121,7 @@ when `labelClusters` is set to TRUE. Default 3.5.}

 \item{legendTitleSize}{size of legend title. Default 12.}

-\item{legendSize}{size of legend. Default 10.

+\item{legendSize}{size of legend. Default NULL.

 Default FALSE.}

 \item{combinePlot}{Must be either "all", "sample", or "none". "all" will combine all plots into a single

@@ -31,6 +31,7 @@ plotSCEDimReduceColData(

   title = NULL,

   titleSize = 15,

   labelClusters = TRUE,

+  clusterLabelSize = 3.5,

   legendTitle = NULL,

   legendTitleSize = NULL,

   legendSize = NULL,

@@ -109,6 +110,9 @@ Default 'blue'.}

 \item{labelClusters}{Logical. Whether the cluster labels are plotted.}

+\item{clusterLabelSize}{Numeric. Determines the size of cluster label

+when `labelClusters` is set to TRUE. Default 3.5.}

+

 \item{legendTitle}{title of legend. Default NULL.}

 \item{legendTitleSize}{size of legend title. Default 12.}

@@ -14,8 +14,9 @@ plotSCEDimReduceColData(

   shape = NULL,

   xlab = NULL,

   ylab = NULL,

-  axisSize = 10,

-  axisLabelSize = 10,

+  baseSize = 12,

+  axisSize = NULL,

+  axisLabelSize = NULL,

   dim1 = NULL,

   dim2 = NULL,

   bin = NULL,

@@ -31,8 +32,8 @@ plotSCEDimReduceColData(

   titleSize = 15,

   labelClusters = TRUE,

   legendTitle = NULL,

-  legendTitleSize = 12,

-  legendSize = 10,

+  legendTitleSize = NULL,

+  legendSize = NULL,

   combinePlot = "none",

   plotLabels = NULL

 )

@@ -6,12 +6,12 @@

 \usage{

 plotSCEDimReduceColData(

   inSCE,

-  sample = NULL,

   colorBy,

+  reducedDimName,

+  sample = NULL,

   groupBy = NULL,

   conditionClass = NULL,

   shape = NULL,

-  reducedDimName = NULL,

   xlab = NULL,

   ylab = NULL,

   axisSize = 10,

@@ -39,13 +39,16 @@ plotSCEDimReduceColData(

 }

 \arguments{

 \item{inSCE}{Input \linkS4class{SingleCellExperiment} object with saved

-dimension reduction components or a variable with saved results. Required}

-

-\item{sample}{Character vector. Indicates which sample each cell belongs to.}

+dimension reduction components or a variable with saved results. Required.}

 \item{colorBy}{Color by a condition(any column of the annotation data).

 Required.}

+\item{reducedDimName}{Saved dimension reduction matrix name in the

+\linkS4class{SingleCellExperiment} object. Required.}

+

+\item{sample}{Character vector. Indicates which sample each cell belongs to.}

+

 \item{groupBy}{Group by a condition(any column of the annotation data).

 Default NULL.}

@@ -55,9 +58,6 @@ original class. Default NULL.}

 \item{shape}{Add shapes to each condition.}

-\item{reducedDimName}{Saved dimension reduction matrix name in the

-\linkS4class{SingleCellExperiment} object. Required.}

-

 \item{xlab}{Character vector. Label for x-axis. Default NULL.}

 \item{ylab}{Character vector. Label for y-axis. Default NULL.}

@@ -122,7 +122,7 @@ Default FALSE.}

 as the labels. If set to "none", no label will be plotted.}

 }

 \value{

-a ggplot of the reduced dimensions.

+a ggplot of the reduced dimension plot of coldata.

 }

 \description{

 Plot results of reduced dimensions data and

@@ -33,7 +33,7 @@ plotSCEDimReduceColData(

   legendTitle = NULL,

   legendTitleSize = 12,

   legendSize = 10,

-  combinePlot = NULL,

+  combinePlot = "none",

   plotLabels = NULL

 )

 }

@@ -115,9 +115,8 @@ Default 'blue'.}

 \item{legendSize}{size of legend. Default 10.

 Default FALSE.}

-\item{combinePlot}{Boolean. If multiple plots are generated (multiple

-samples, etc.), will combined plots using `cowplot::plot_grid`.

-Default TRUE.}

+\item{combinePlot}{Must be either "all", "sample", or "none". "all" will combine all plots into a single

+.ggplot object, while "sample" will output a list of plots separated by sample. Default "none".}

 \item{plotLabels}{labels to each plot. If set to "default", will use the name of the samples

 as the labels. If set to "none", no label will be plotted.}

@@ -14,8 +14,8 @@ plotSCEDimReduceColData(

   reducedDimName = NULL,

   xlab = NULL,

   ylab = NULL,

-  axisSize = 10,

-  axisLabelSize = 10,

+  axisSize = NULL,

+  axisLabelSize = NULL,

   dim1 = NULL,

   dim2 = NULL,

   bin = NULL,

@@ -33,7 +33,8 @@ plotSCEDimReduceColData(

   legendTitle = NULL,

   legendTitleSize = 12,

   legendSize = 10,

-  combinePlot = TRUE

+  combinePlot = NULL,

+  plotLabels = NULL

 )

 }

 \arguments{

@@ -117,6 +118,9 @@ Default FALSE.}

 \item{combinePlot}{Boolean. If multiple plots are generated (multiple

 samples, etc.), will combined plots using `cowplot::plot_grid`.

 Default TRUE.}

+

+\item{plotLabels}{labels to each plot. If set to "default", will use the name of the samples

+as the labels. If set to "none", no label will be plotted.}

 }

 \value{

 a ggplot of the reduced dimensions.

@@ -32,7 +32,8 @@ plotSCEDimReduceColData(

   labelClusters = TRUE,

   legendTitle = NULL,

   legendTitleSize = 12,

-  legendSize = 10

+  legendSize = 10,

+  combinePlot = TRUE

 )

 }

 \arguments{

@@ -112,6 +113,10 @@ Default 'blue'.}

 \item{legendSize}{size of legend. Default 10.

 Default FALSE.}

+

+\item{combinePlot}{Boolean. If multiple plots are generated (multiple

+samples, etc.), will combined plots using `cowplot::plot_grid`.

+Default TRUE.}

 }

 \value{

 a ggplot of the reduced dimensions.

@@ -22,6 +22,7 @@ plotSCEDimReduceColData(

   binLabel = NULL,

   dotSize = 2,

   transparency = 1,

+  colorScale = NULL,

   colorLow = "white",

   colorMid = "gray",

   colorHigh = "blue",

@@ -81,6 +82,10 @@ Default NULL.}

 \item{transparency}{Transparency of the dots, values will be 0-1. Default 1.}

+\item{colorScale}{Vector. Needs to be same length as the

+number of unique levels of colorBy. Will be used only if

+conditionClass = "factor" or "character". Default NULL.}

+

 \item{colorLow}{Character. A color available from `colors()`.

 The color will be used to signify the lowest values on the scale.

 Default 'white'.}

@@ -14,6 +14,8 @@ plotSCEDimReduceColData(

   reducedDimName = NULL,

   xlab = NULL,

   ylab = NULL,

+  axisSize = 10,

+  axisLabelSize = 10,

   dim1 = NULL,

   dim2 = NULL,

   bin = NULL,

@@ -27,7 +29,9 @@ plotSCEDimReduceColData(

   title = NULL,

   titleSize = 15,

   labelClusters = TRUE,

-  legendTitle = NULL

+  legendTitle = NULL,

+  legendTitleSize = 12,

+  legendSize = 10

 )

 }

 \arguments{

@@ -55,6 +59,10 @@ original class. Default NULL.}

 \item{ylab}{Character vector. Label for y-axis. Default NULL.}

+\item{axisSize}{Size of x/y-axis ticks. Default 10.}

+

+\item{axisLabelSize}{Size of x/y-axis labels. Default 10.}

+

 \item{dim1}{1st dimension to be used for plotting. Can either be a string which specifies

 the name of the dimension to be plotted from reducedDims, or a numeric value which specifies

 the index of the dimension to be plotted. Default is NULL.}

@@ -93,7 +101,11 @@ Default 'blue'.}

 \item{labelClusters}{Logical. Whether the cluster labels are plotted.}

-\item{legendTitle}{title of legend. Default NULL.

+\item{legendTitle}{title of legend. Default NULL.}

+

+\item{legendTitleSize}{size of legend title. Default 12.}

+

+\item{legendSize}{size of legend. Default 10.

 Default FALSE.}

 }

 \value{

@@ -31,8 +31,8 @@ plotSCEDimReduceColData(

 )

 }

 \arguments{

-\item{inSCE}{Input SCtkExperiment object with saved dimension reduction

-components or a variable with saved results. Required}

+\item{inSCE}{Input \linkS4class{SingleCellExperiment} object with saved

+dimension reduction components or a variable with saved results. Required}

 \item{sample}{Character vector. Indicates which sample each cell belongs to.}

@@ -48,8 +48,8 @@ original class. Default NULL.}

 \item{shape}{Add shapes to each condition.}

-\item{reducedDimName}{Saved dimension reduction matrix name in the SCtkExperiment

-object. Required.}

+\item{reducedDimName}{Saved dimension reduction matrix name in the

+\linkS4class{SingleCellExperiment} object. Required.}

 \item{xlab}{Character vector. Label for x-axis. Default NULL.}

@@ -8,6 +8,7 @@ plotSCEDimReduceColData(

   inSCE,

   sample = NULL,

   colorBy,

+  groupBy = NULL,

   conditionClass = NULL,

   shape = NULL,

   reducedDimName = NULL,

@@ -38,6 +39,9 @@ components or a variable with saved results. Required}

 \item{colorBy}{Color by a condition(any column of the annotation data).

 Required.}

+\item{groupBy}{Group by a condition(any column of the annotation data).

+Default NULL.}

+

 \item{conditionClass}{Class of the annotation data used in colorBy.

 Options are NULL, "factor" or "numeric". If NULL, class will default to the

 original class. Default NULL.}

@@ -19,6 +19,9 @@ plotSCEDimReduceColData(

   binLabel = NULL,

   dotSize = 2,

   transparency = 1,

+  colorLow = "white",

+  colorMid = "gray",

+  colorHigh = "blue",

   defaultTheme = TRUE,

   title = NULL,

   titleSize = 15,

@@ -66,6 +69,18 @@ Default NULL.}

 \item{transparency}{Transparency of the dots, values will be 0-1. Default 1.}

+\item{colorLow}{Character. A color available from `colors()`.

+The color will be used to signify the lowest values on the scale.

+Default 'white'.}

+

+\item{colorMid}{Character. A color available from `colors()`.

+The color will be used to signify the midpoint on the scale.

+Default 'gray'.}

+

+\item{colorHigh}{Character. A color available from `colors()`.

+The color will be used to signify the highest values on the scale.

+Default 'blue'.}

+

 \item{defaultTheme}{adds grid to plot when TRUE. Default TRUE.}

 \item{title}{Title of plot. Default NULL.}

@@ -17,7 +17,7 @@ plotSCEDimReduceColData(

   dim2 = NULL,

   bin = NULL,

   binLabel = NULL,

-  dotsize = 2,

+  dotSize = 2,

   transparency = 1,

   defaultTheme = TRUE,

   title = NULL,

@@ -62,7 +62,7 @@ If more than one value, will bin numeric values using values as a cut point.}

 \item{binLabel}{Character vector. Labels for the bins created by the `bin` parameter.

 Default NULL.}

-\item{dotsize}{Size of dots. Default 2.}

+\item{dotSize}{Size of dots. Default 2.}

 \item{transparency}{Transparency of the dots, values will be 0-1. Default 1.}

@@ -95,7 +95,7 @@ plotSCEDimReduceColData(

 plotSCEDimReduceColData(

   inSCE = mouseBrainSubsetSCE, colorBy = "age",

   shape = NULL, conditionClass = "numeric",

-  reducedDimName = "TSNE_counts", bin =  c(-Inf,20,25,+Inf),

+  reducedDimName = "TSNE_counts", bin = c(-Inf, 20, 25, +Inf),

   xlab = "tSNE1", ylab = "tSNE2", labelClusters = FALSE

 )

 }

@@ -6,6 +6,7 @@

 \usage{

 plotSCEDimReduceColData(

   inSCE,

+  sample = NULL,

   colorBy,

   conditionClass = NULL,

   shape = NULL,

@@ -29,6 +30,8 @@ plotSCEDimReduceColData(

 \item{inSCE}{Input SCtkExperiment object with saved dimension reduction

 components or a variable with saved results. Required}

+\item{sample}{Character vector. Indicates which sample each cell belongs to.}

+

 \item{colorBy}{Color by a condition(any column of the annotation data).

 Required.}

@@ -6,14 +6,16 @@

 \usage{

 plotSCEDimReduceColData(

   inSCE,

-  colorBy = "No Color",

-  shape = "No Shape",

-  reducedDimName = NULL,

+  colorBy,

   conditionClass = NULL,

+  shape = NULL,

+  reducedDimName = NULL,

   xlab = NULL,

   ylab = NULL,

   dim1 = NULL,

   dim2 = NULL,

+  bin = NULL,

+  binLabel = NULL,

   dotsize = 2,

   transparency = 1,

   defaultTheme = TRUE,

@@ -27,34 +29,45 @@ plotSCEDimReduceColData(

 \item{inSCE}{Input SCtkExperiment object with saved dimension reduction

 components or a variable with saved results. Required}

-\item{colorBy}{color by a condition(any column of the annotation data).}

+\item{colorBy}{Color by a condition(any column of the annotation data).

+Required.}

+

+\item{conditionClass}{Class of the annotation data used in colorBy.

+Options are NULL, "factor" or "numeric". If NULL, class will default to the

+original class. Default NULL.}

-\item{shape}{add shapes to each condition.}

+\item{shape}{Add shapes to each condition.}

-\item{reducedDimName}{saved dimension reduction name in the SCtkExperiment

+\item{reducedDimName}{Saved dimension reduction matrix name in the SCtkExperiment

 object. Required.}

-\item{conditionClass}{class of the annotation data used in colorBy.

-Options are NULL, "factor" or "numeric". If NULL, class will default to the

-original class. Default NULL.}

+\item{xlab}{Character vector. Label for x-axis. Default NULL.}

+

+\item{ylab}{Character vector. Label for y-axis. Default NULL.}

-\item{xlab}{label for x-axis}

+\item{dim1}{1st dimension to be used for plotting. Can either be a string which specifies

+the name of the dimension to be plotted from reducedDims, or a numeric value which specifies

+the index of the dimension to be plotted. Default is NULL.}

-\item{ylab}{label for y-axis}

+\item{dim2}{2nd dimension to be used for plotting. Can either be a string which specifies

+the name of the dimension to be plotted from reducedDims, or a numeric value which specifies

+the index of the dimension to be plotted. Default is NULL.}

-\item{dim1}{1st dimension to be used for plotting. Default is NULL.}

+\item{bin}{Numeric vector. If single value, will divide the numeric values into the `bin` groups.

+If more than one value, will bin numeric values using values as a cut point.}

-\item{dim2}{2nd dimension to be used for plotting. Default is NULL.}

+\item{binLabel}{Character vector. Labels for the bins created by the `bin` parameter.

+Default NULL.}

-\item{dotsize}{size of dots. Default 2.}

+\item{dotsize}{Size of dots. Default 2.}

-\item{transparency}{transparency of the dots, values will be 0-1. Default 1.}

+\item{transparency}{Transparency of the dots, values will be 0-1. Default 1.}

 \item{defaultTheme}{adds grid to plot when TRUE. Default TRUE.}

-\item{title}{title of plot. Default NULL.}

+\item{title}{Title of plot. Default NULL.}

-\item{titleSize}{size of title of plot. Default 15.}

+\item{titleSize}{Size of title of plot. Default 15.}

 \item{labelClusters}{Logical. Whether the cluster labels are plotted.}

@@ -71,8 +84,15 @@ Plot results of reduced dimensions data and

 \examples{

 plotSCEDimReduceColData(

   inSCE = mouseBrainSubsetSCE, colorBy = "tissue",

-  shape = "No Shape", conditionClass = "factor",

+  shape = NULL, conditionClass = "factor",

   reducedDimName = "TSNE_counts",

   xlab = "tSNE1", ylab = "tSNE2", labelClusters = TRUE

 )

+

+plotSCEDimReduceColData(

+  inSCE = mouseBrainSubsetSCE, colorBy = "age",

+  shape = NULL, conditionClass = "numeric",

+  reducedDimName = "TSNE_counts", bin =  c(-Inf,20,25,+Inf),

+  xlab = "tSNE1", ylab = "tSNE2", labelClusters = FALSE

+)

 }

new file mode 100644

@@ -0,0 +1,78 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/ggPlotting.R

+\name{plotSCEDimReduceColData}

+\alias{plotSCEDimReduceColData}

+\title{Dimension reduction plot tool for colData}

+\usage{

+plotSCEDimReduceColData(

+  inSCE,

+  colorBy = "No Color",

+  shape = "No Shape",

+  reducedDimName = NULL,

+  conditionClass = NULL,

+  xlab = NULL,

+  ylab = NULL,

+  dim1 = NULL,

+  dim2 = NULL,

+  dotsize = 2,

+  transparency = 1,

+  defaultTheme = TRUE,

+  title = NULL,

+  titleSize = 15,

+  labelClusters = TRUE,

+  legendTitle = NULL

+)

+}

+\arguments{

+\item{inSCE}{Input SCtkExperiment object with saved dimension reduction

+components or a variable with saved results. Required}

+

+\item{colorBy}{color by a condition(any column of the annotation data).}

+

+\item{shape}{add shapes to each condition.}

+

+\item{reducedDimName}{saved dimension reduction name in the SCtkExperiment

+object. Required.}

+

+\item{conditionClass}{class of the annotation data used in colorBy.

+Options are NULL, "factor" or "numeric". If NULL, class will default to the

+original class. Default NULL.}

+

+\item{xlab}{label for x-axis}

+

+\item{ylab}{label for y-axis}

+

+\item{dim1}{1st dimension to be used for plotting. Default is NULL.}

+

+\item{dim2}{2nd dimension to be used for plotting. Default is NULL.}

+

+\item{dotsize}{size of dots. Default 2.}

+

+\item{transparency}{transparency of the dots, values will be 0-1. Default 1.}

+

+\item{defaultTheme}{adds grid to plot when TRUE. Default TRUE.}

+

+\item{title}{title of plot. Default NULL.}

+

+\item{titleSize}{size of title of plot. Default 15.}

+

+\item{labelClusters}{Logical. Whether the cluster labels are plotted.}

+

+\item{legendTitle}{title of legend. Default NULL.

+Default FALSE.}

+}

+\value{

+a ggplot of the reduced dimensions.

+}

+\description{

+Plot results of reduced dimensions data and

+ colors by annotation data stored in the colData slot.

+}

+\examples{

+plotSCEDimReduceColData(

+  inSCE = mouseBrainSubsetSCE, colorBy = "tissue",

+  shape = "No Shape", conditionClass = "factor",

+  reducedDimName = "TSNE_counts",

+  xlab = "tSNE1", ylab = "tSNE2", labelClusters = TRUE

+)

+}