1. singleCellTK
  2. man
  3. plotBarcodeRankScatter.Rd
Browse code

Tweaking the default size parameters some plotting functions

Joshua D. Campbell authored on 20/01/2023 17:26:28
Showing 1 changed files
man/plotBarcodeRankScatter.Rd
History View file @ 9ff358be
... ... 
@@ -8,7 +8,7 @@ plotBarcodeRankScatter(
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   inSCE,
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   sample = NULL,
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   defaultTheme = TRUE,
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-  dotSize = 0.5,
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+  dotSize = 0.1,
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   title = NULL,
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   titleSize = 18,
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   xlab = NULL,
... ... 
@@ -32,7 +32,7 @@ sample each cell belongs to. Default \code{NULL}.}
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 \item{defaultTheme}{Removes grid in plot and sets axis title size to
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 \code{10} when \code{TRUE}. Default \code{TRUE}.}
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-\item{dotSize}{Size of dots. Default \code{0.5}.}
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+\item{dotSize}{Size of dots. Default \code{0.1}.}
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 \item{title}{Title of plot. Default \code{NULL}.}
38 38
Browse code

Update barcodeRank and EmptyDrops

Yichen Wang authored on 14/10/2022 09:54:10
Showing 1 changed files
man/plotBarcodeRankScatter.Rd
History View file @ 229625bd
... ... 
@@ -24,39 +24,40 @@ plotBarcodeRankScatter(
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 \arguments{
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 \item{inSCE}{Input \linkS4class{SingleCellExperiment} object with saved
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 dimension reduction components or a variable with saved results from
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-\link{runBarcodeRankDrops}. Required.}
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+\code{\link{runBarcodeRankDrops}}. Required.}
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-\item{sample}{Character vector. Indicates which sample each cell belongs to.
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-Default NULL.}
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+\item{sample}{Character vector or colData variable name. Indicates which
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+sample each cell belongs to. Default \code{NULL}.}
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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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+\item{defaultTheme}{Removes grid in plot and sets axis title size to
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+\code{10} when \code{TRUE}. Default \code{TRUE}.}
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-\item{dotSize}{Size of dots. Default 0.5.}
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+\item{dotSize}{Size of dots. Default \code{0.5}.}
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-\item{title}{Title of plot. Default NULL.}
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+\item{title}{Title of plot. Default \code{NULL}.}
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-\item{titleSize}{Size of title of plot. Default 18.}
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+\item{titleSize}{Size of title of plot. Default \code{18}.}
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-\item{xlab}{Character vector. Label for x-axis. Default NULL.}
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+\item{xlab}{Character vector. Label for x-axis. Default \code{NULL}.}
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-\item{ylab}{Character vector. Label for y-axis. Default NULL.}
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+\item{ylab}{Character vector. Label for y-axis. Default \code{NULL}.}
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-\item{axisSize}{Size of x/y-axis ticks. Default 12.}
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+\item{axisSize}{Size of x/y-axis ticks. Default \code{12}.}
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-\item{axisLabelSize}{Size of x/y-axis labels. Default 15.}
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+\item{axisLabelSize}{Size of x/y-axis labels. Default \code{15}.}
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-\item{legendSize}{size of legend. Default 10.}
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+\item{legendSize}{size of legend. Default \code{10}.}
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-\item{combinePlot}{Boolean. If multiple plots are generated (multiple
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-samples, etc.), will combined plots using `cowplot::plot_grid`.}
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+\item{combinePlot}{Must be either \code{"all"}, \code{"sample"}, or
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+\code{"none"}. \code{"all"} will combine all plots into a single .ggplot
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+object, while \code{"sample"} will output a list of plots separated by
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+sample. Default \code{"all"}.}
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-\item{sampleRelHeights}{If there are multiple samples and combining by "all",
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-the relative heights for each plot.}
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+\item{sampleRelHeights}{If there are multiple samples and combining by
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+\code{"all"}, the relative heights for each plot. Default \code{1}.}
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-\item{sampleRelWidths}{If there are multiple samples and combining by "all",
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-the relative widths for each plot.
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-Default TRUE.}
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+\item{sampleRelWidths}{If there are multiple samples and combining by
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+\code{"all"}, the relative widths for each plot. Default \code{1}.}
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 }
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 \value{
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 a ggplot object of the scatter plot.
... ... 
@@ -67,7 +68,11 @@ A plotting function which visualizes outputs from the
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  object via scatterplot.
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 }
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 \examples{
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-data(scExample, package="singleCellTK")
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-sce <- runBarcodeRankDrops(inSCE=sce)
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-plotBarcodeRankScatter(inSCE=sce)
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+data(scExample, package = "singleCellTK")
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+sce <- runBarcodeRankDrops(inSCE = sce)
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+plotBarcodeRankScatter(inSCE = sce)
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+}
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+\seealso{
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+\code{\link{plotBarcodeRankDropsResults}},
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+\code{\link{runBarcodeRankDrops}}
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 }
Browse code

Change default reducedDimName settings, DecontX functions use 'decontX_UMAP'

Yusuke Koga authored on 22/09/2021 13:09:56
Showing 1 changed files
man/plotBarcodeRankScatter.Rd
History View file @ 94e4e060
... ... 
@@ -8,7 +8,7 @@ plotBarcodeRankScatter(
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   inSCE,
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   sample = NULL,
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   defaultTheme = TRUE,
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-  dotSize = 1,
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+  dotSize = 0.5,
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   title = NULL,
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   titleSize = 18,
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   xlab = NULL,
... ... 
@@ -32,7 +32,7 @@ Default NULL.}
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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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-\item{dotSize}{Size of dots. Default 1.}
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+\item{dotSize}{Size of dots. Default 0.5.}
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 \item{title}{Title of plot. Default NULL.}
38 38
Browse code

Add value sections to documentation

Yusuke Koga authored on 15/10/2020 23:39:34
Showing 1 changed files
man/plotBarcodeRankScatter.Rd
History View file @ 09571895
... ... 
@@ -58,6 +58,9 @@ the relative heights for each plot.}
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 the relative widths for each plot.
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 Default TRUE.}
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 }
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+\value{
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+a ggplot object of the scatter plot.
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+}
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 \description{
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 A plotting function which visualizes outputs from the
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  runBarcodeRankDrops function stored in the colData slot of the SingleCellExperiment
Browse code

Additional bug fixes relevant to ggSCTKCombinePlots function

Yusuke Koga authored on 07/10/2020 08:19:03
Showing 1 changed files
man/plotBarcodeRankScatter.Rd
History View file @ ad15d591
... ... 
@@ -16,7 +16,7 @@ plotBarcodeRankScatter(
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   axisSize = 12,
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   axisLabelSize = 15,
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   legendSize = 10,
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-  combinePlot = NULL,
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+  combinePlot = "none",
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   sampleRelHeights = 1,
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   sampleRelWidths = 1
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 )
Browse code

Debug .ggSCTKCombinePlots

Yusuke Koga authored on 23/09/2020 12:09:09
Showing 1 changed files
man/plotBarcodeRankScatter.Rd
History View file @ 75f463fa
... ... 
@@ -16,7 +16,9 @@ plotBarcodeRankScatter(
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   axisSize = 12,
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   axisLabelSize = 15,
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   legendSize = 10,
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-  combinePlot = TRUE
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+  combinePlot = NULL,
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+  sampleRelHeights = 1,
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+  sampleRelWidths = 1
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 )
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 }
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 \arguments{
... ... 
@@ -47,7 +49,13 @@ when TRUE. Default TRUE.}
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 \item{legendSize}{size of legend. Default 10.}
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 \item{combinePlot}{Boolean. If multiple plots are generated (multiple
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-samples, etc.), will combined plots using `cowplot::plot_grid`.
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+samples, etc.), will combined plots using `cowplot::plot_grid`.}
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+
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+\item{sampleRelHeights}{If there are multiple samples and combining by "all",
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+the relative heights for each plot.}
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+
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+\item{sampleRelWidths}{If there are multiple samples and combining by "all",
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+the relative widths for each plot.
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 Default TRUE.}
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 }
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 \description{
Browse code

Add combinePlot parameter

Yusuke Koga authored on 29/07/2020 14:30:24
Showing 1 changed files
man/plotBarcodeRankScatter.Rd
History View file @ d23bcd51
... ... 
@@ -15,7 +15,8 @@ plotBarcodeRankScatter(
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   ylab = NULL,
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   axisSize = 12,
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   axisLabelSize = 15,
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-  legendSize = 10
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+  legendSize = 10,
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+  combinePlot = TRUE
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 )
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 }
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 \arguments{
... ... 
@@ -44,6 +45,10 @@ when TRUE. Default TRUE.}
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 \item{axisLabelSize}{Size of x/y-axis labels. Default 15.}
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 \item{legendSize}{size of legend. Default 10.}
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+
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+\item{combinePlot}{Boolean. If multiple plots are generated (multiple
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+samples, etc.), will combined plots using `cowplot::plot_grid`.
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+Default TRUE.}
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 }
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 \description{
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 A plotting function which visualizes outputs from the
Browse code

Update DESCRIPTION

Yusuke Koga authored on 14/07/2020 21:49:17
Showing 1 changed files
man/plotBarcodeRankScatter.Rd
History View file @ 8c91ccd9
... ... 
@@ -2,7 +2,7 @@
2 2 
 % Please edit documentation in R/ggPlotting.R
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 \name{plotBarcodeRankScatter}
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 \alias{plotBarcodeRankScatter}
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-\title{Plots for runEmptyDrops outputs.}
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+\title{Plots for runBarcodeRankDrops outputs.}
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 \usage{
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 plotBarcodeRankScatter(
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   inSCE,
... ... 
@@ -21,7 +21,7 @@ plotBarcodeRankScatter(
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 \arguments{
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 \item{inSCE}{Input \linkS4class{SingleCellExperiment} object with saved
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 dimension reduction components or a variable with saved results from
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-\link{runScrublet}. Required.}
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+\link{runBarcodeRankDrops}. Required.}
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 \item{sample}{Character vector. Indicates which sample each cell belongs to.
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 Default NULL.}
... ... 
@@ -47,7 +47,7 @@ when TRUE. Default TRUE.}
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 }
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 \description{
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 A plotting function which visualizes outputs from the
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- runEmptyDrops function stored in the colData slot of the SingleCellExperiment
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+ runBarcodeRankDrops function stored in the colData slot of the SingleCellExperiment
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  object via scatterplot.
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 }
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 \examples{
Browse code

Edits to plotting fxn for droplet based fxns

Yusuke Koga authored on 14/07/2020 18:20:53
Showing 1 changed files
man/plotBarcodeRankScatter.Rd
History View file @ dea0dc42
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,57 @@
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/ggPlotting.R
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+\name{plotBarcodeRankScatter}
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+\alias{plotBarcodeRankScatter}
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+\title{Plots for runEmptyDrops outputs.}
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+\usage{
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+plotBarcodeRankScatter(
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+  inSCE,
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+  sample = NULL,
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+  defaultTheme = TRUE,
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+  dotSize = 1,
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+  title = NULL,
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+  titleSize = 18,
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+  xlab = NULL,
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+  ylab = NULL,
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+  axisSize = 12,
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+  axisLabelSize = 15,
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+  legendSize = 10
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+)
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+}
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+\arguments{
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+\item{inSCE}{Input \linkS4class{SingleCellExperiment} object with saved
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+dimension reduction components or a variable with saved results from
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+\link{runScrublet}. Required.}
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+
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+\item{sample}{Character vector. Indicates which sample each cell belongs to.
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+Default NULL.}
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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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+
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+\item{dotSize}{Size of dots. Default 1.}
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+
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+\item{title}{Title of plot. Default NULL.}
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+
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+\item{titleSize}{Size of title of plot. Default 18.}
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+
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+\item{xlab}{Character vector. Label for x-axis. Default NULL.}
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+
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+\item{ylab}{Character vector. Label for y-axis. Default NULL.}
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+
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+\item{axisSize}{Size of x/y-axis ticks. Default 12.}
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+
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+\item{axisLabelSize}{Size of x/y-axis labels. Default 15.}
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+
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+\item{legendSize}{size of legend. Default 10.}
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+}
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+\description{
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+A plotting function which visualizes outputs from the
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+ runEmptyDrops function stored in the colData slot of the SingleCellExperiment
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+ object via scatterplot.
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+}
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+\examples{
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+data(scExample, package="singleCellTK")
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+sce <- runBarcodeRankDrops(inSCE=sce)
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+plotBarcodeRankScatter(inSCE=sce)
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+}