Akshay Aravind authored on 29/01/2024 18:28:20
| ... | ... |
@@ -24,14 +24,14 @@ computations.} |
| 24 | 24 |
\code{"dispersion"} or \code{"modelGeneVar"}.}
|
| 25 | 25 |
|
| 26 | 26 |
\item{hvgNumber}{Specify the number of top genes to highlight in red. Default
|
| 27 |
-\code{NULL}. See details.}
|
|
| 27 |
+\code{2000}. See details.}
|
|
| 28 | 28 |
|
| 29 | 29 |
\item{useFeatureSubset}{A character string for the \code{rowData} variable
|
| 30 | 30 |
name to store a logical index of selected features. Default \code{NULL}. See
|
| 31 | 31 |
details.} |
| 32 | 32 |
|
| 33 | 33 |
\item{labelsCount}{Specify the number of data points/genes to label. Should
|
| 34 |
-be less than \code{hvgNumber}. Default \code{20}. See details.}
|
|
| 34 |
+be less than \code{hvgNumber}. Default \code{10}. See details.}
|
|
| 35 | 35 |
|
| 36 | 36 |
\item{featureDisplay}{A character string for the \code{rowData} variable name
|
| 37 | 37 |
to indicate what type of feature ID should be displayed. If set by |
Akshay Aravind authored on 29/01/2024 18:19:13
| ... | ... |
@@ -6,10 +6,10 @@ |
| 6 | 6 |
\usage{
|
| 7 | 7 |
plotTopHVG( |
| 8 | 8 |
inSCE, |
| 9 |
- method = c("vst", "mean.var.plot", "dispersion", "modelGeneVar"),
|
|
| 10 |
- hvgNumber = NULL, |
|
| 9 |
+ method = "modelGeneVar", |
|
| 10 |
+ hvgNumber = 2000, |
|
| 11 | 11 |
useFeatureSubset = NULL, |
| 12 |
- labelsCount = 20, |
|
| 12 |
+ labelsCount = 10, |
|
| 13 | 13 |
featureDisplay = metadata(inSCE)$featureDisplay, |
| 14 | 14 |
labelSize = 2, |
| 15 | 15 |
dotSize = 2, |
Yichen Wang authored on 23/09/2022 04:25:14
| ... | ... |
@@ -10,30 +10,41 @@ plotTopHVG( |
| 10 | 10 |
hvgNumber = NULL, |
| 11 | 11 |
useFeatureSubset = NULL, |
| 12 | 12 |
labelsCount = 20, |
| 13 |
- featureDisplay = metadata(inSCE)$featureDisplay |
|
| 13 |
+ featureDisplay = metadata(inSCE)$featureDisplay, |
|
| 14 |
+ labelSize = 2, |
|
| 15 |
+ dotSize = 2, |
|
| 16 |
+ textSize = 12 |
|
| 14 | 17 |
) |
| 15 | 18 |
} |
| 16 | 19 |
\arguments{
|
| 17 | 20 |
\item{inSCE}{Input \code{SingleCellExperiment} object containing the
|
| 18 | 21 |
computations.} |
| 19 | 22 |
|
| 20 |
-\item{method}{Select either \code{"vst"}, \code{"mean.var.plot"},
|
|
| 23 |
+\item{method}{Select either \code{"vst"}, \code{"mean.var.plot"},
|
|
| 21 | 24 |
\code{"dispersion"} or \code{"modelGeneVar"}.}
|
| 22 | 25 |
|
| 23 | 26 |
\item{hvgNumber}{Specify the number of top genes to highlight in red. Default
|
| 24 | 27 |
\code{NULL}. See details.}
|
| 25 | 28 |
|
| 26 |
-\item{useFeatureSubset}{A character string for the \code{rowData} variable
|
|
| 27 |
-name to store a logical index of selected features. Default \code{NULL}. See
|
|
| 29 |
+\item{useFeatureSubset}{A character string for the \code{rowData} variable
|
|
| 30 |
+name to store a logical index of selected features. Default \code{NULL}. See
|
|
| 28 | 31 |
details.} |
| 29 | 32 |
|
| 30 |
-\item{labelsCount}{Specify the number of data points/genes to label. Should
|
|
| 33 |
+\item{labelsCount}{Specify the number of data points/genes to label. Should
|
|
| 31 | 34 |
be less than \code{hvgNumber}. Default \code{20}. See details.}
|
| 32 | 35 |
|
| 33 | 36 |
\item{featureDisplay}{A character string for the \code{rowData} variable name
|
| 34 |
-to indicate what type of feature ID should be displayed. If set by |
|
| 37 |
+to indicate what type of feature ID should be displayed. If set by |
|
| 35 | 38 |
\code{\link{setSCTKDisplayRow}}, will by default use it. If \code{NULL}, will
|
| 36 | 39 |
use \code{rownames(inSCE)}.}
|
| 40 |
+ |
|
| 41 |
+\item{labelSize}{Numeric, size of the text label on top HVGs. Default
|
|
| 42 |
+\code{2}.}
|
|
| 43 |
+ |
|
| 44 |
+\item{dotSize}{Numeric, size of the dots of the features. Default \code{2}.}
|
|
| 45 |
+ |
|
| 46 |
+\item{textSize}{Numeric, size of the text of axis title, axis label, etc.
|
|
| 47 |
+Default \code{12}.}
|
|
| 37 | 48 |
} |
| 38 | 49 |
\value{
|
| 39 | 50 |
ggplot of HVG metrics and top HVG labels |
| ... | ... |
@@ -44,9 +55,9 @@ Plot highly variable genes |
| 44 | 55 |
\details{
|
| 45 | 56 |
When \code{hvgNumber = NULL} and \code{useFeature = NULL}, only plot
|
| 46 | 57 |
the mean VS variance/dispersion scatter plot. When only \code{hvgNumber} set,
|
| 47 |
-label the top \code{hvgNumber} HVGs ranked by the metrics calculated by
|
|
| 48 |
-\code{method}. When \code{useFeatureSubset} set, label the features in
|
|
| 49 |
-the subset on the scatter plot created with \code{method} and ignore
|
|
| 58 |
+label the top \code{hvgNumber} HVGs ranked by the metrics calculated by
|
|
| 59 |
+\code{method}. When \code{useFeatureSubset} set, label the features in
|
|
| 60 |
+the subset on the scatter plot created with \code{method} and ignore
|
|
| 50 | 61 |
\code{hvgNumber}.
|
| 51 | 62 |
} |
| 52 | 63 |
\examples{
|
Yichen Wang authored on 30/05/2022 22:53:42
| ... | ... |
@@ -7,7 +7,8 @@ |
| 7 | 7 |
plotTopHVG( |
| 8 | 8 |
inSCE, |
| 9 | 9 |
method = c("vst", "mean.var.plot", "dispersion", "modelGeneVar"),
|
| 10 |
- hvgNumber = 2000, |
|
| 10 |
+ hvgNumber = NULL, |
|
| 11 |
+ useFeatureSubset = NULL, |
|
| 11 | 12 |
labelsCount = 20, |
| 12 | 13 |
featureDisplay = metadata(inSCE)$featureDisplay |
| 13 | 14 |
) |
| ... | ... |
@@ -20,10 +21,14 @@ computations.} |
| 20 | 21 |
\code{"dispersion"} or \code{"modelGeneVar"}.}
|
| 21 | 22 |
|
| 22 | 23 |
\item{hvgNumber}{Specify the number of top genes to highlight in red. Default
|
| 23 |
-\code{2000}.}
|
|
| 24 |
+\code{NULL}. See details.}
|
|
| 25 |
+ |
|
| 26 |
+\item{useFeatureSubset}{A character string for the \code{rowData} variable
|
|
| 27 |
+name to store a logical index of selected features. Default \code{NULL}. See
|
|
| 28 |
+details.} |
|
| 24 | 29 |
|
| 25 | 30 |
\item{labelsCount}{Specify the number of data points/genes to label. Should
|
| 26 |
-be less than \code{hvgNumber}. Default \code{20}.}
|
|
| 31 |
+be less than \code{hvgNumber}. Default \code{20}. See details.}
|
|
| 27 | 32 |
|
| 28 | 33 |
\item{featureDisplay}{A character string for the \code{rowData} variable name
|
| 29 | 34 |
to indicate what type of feature ID should be displayed. If set by |
| ... | ... |
@@ -31,11 +36,19 @@ to indicate what type of feature ID should be displayed. If set by |
| 31 | 36 |
use \code{rownames(inSCE)}.}
|
| 32 | 37 |
} |
| 33 | 38 |
\value{
|
| 34 |
-ggplot of HVG metrics |
|
| 39 |
+ggplot of HVG metrics and top HVG labels |
|
| 35 | 40 |
} |
| 36 | 41 |
\description{
|
| 37 | 42 |
Plot highly variable genes |
| 38 | 43 |
} |
| 44 |
+\details{
|
|
| 45 |
+When \code{hvgNumber = NULL} and \code{useFeature = NULL}, only plot
|
|
| 46 |
+the mean VS variance/dispersion scatter plot. When only \code{hvgNumber} set,
|
|
| 47 |
+label the top \code{hvgNumber} HVGs ranked by the metrics calculated by
|
|
| 48 |
+\code{method}. When \code{useFeatureSubset} set, label the features in
|
|
| 49 |
+the subset on the scatter plot created with \code{method} and ignore
|
|
| 50 |
+\code{hvgNumber}.
|
|
| 51 |
+} |
|
| 39 | 52 |
\examples{
|
| 40 | 53 |
data("mouseBrainSubsetSCE", package = "singleCellTK")
|
| 41 | 54 |
mouseBrainSubsetSCE <- runModelGeneVar(mouseBrainSubsetSCE) |
Yichen Wang authored on 20/05/2022 14:07:18
| ... | ... |
@@ -7,38 +7,41 @@ |
| 7 | 7 |
plotTopHVG( |
| 8 | 8 |
inSCE, |
| 9 | 9 |
method = c("vst", "mean.var.plot", "dispersion", "modelGeneVar"),
|
| 10 |
- hvgList = NULL, |
|
| 11 |
- n = NULL, |
|
| 12 |
- labelsCount = NULL |
|
| 10 |
+ hvgNumber = 2000, |
|
| 11 |
+ labelsCount = 20, |
|
| 12 |
+ featureDisplay = metadata(inSCE)$featureDisplay |
|
| 13 | 13 |
) |
| 14 | 14 |
} |
| 15 | 15 |
\arguments{
|
| 16 | 16 |
\item{inSCE}{Input \code{SingleCellExperiment} object containing the
|
| 17 | 17 |
computations.} |
| 18 | 18 |
|
| 19 |
-\item{method}{Select either "vst", "mean.var.plot", "dispersion" or
|
|
| 20 |
-"modelGeneVar".} |
|
| 19 |
+\item{method}{Select either \code{"vst"}, \code{"mean.var.plot"},
|
|
| 20 |
+\code{"dispersion"} or \code{"modelGeneVar"}.}
|
|
| 21 | 21 |
|
| 22 |
-\item{hvgList}{Character vector indicating the labels of highly variable
|
|
| 23 |
-genes.} |
|
| 22 |
+\item{hvgNumber}{Specify the number of top genes to highlight in red. Default
|
|
| 23 |
+\code{2000}.}
|
|
| 24 | 24 |
|
| 25 |
-\item{n}{Specify the number of top genes to highlight in red. If
|
|
| 26 |
-\code{hvgList}
|
|
| 27 |
- parameter is not provided, this parameter can be used simply to specify |
|
| 28 |
- the number of top genes to highlight in red.} |
|
| 25 |
+\item{labelsCount}{Specify the number of data points/genes to label. Should
|
|
| 26 |
+be less than \code{hvgNumber}. Default \code{20}.}
|
|
| 29 | 27 |
|
| 30 |
-\item{labelsCount}{Specify the number of data points/genes to label.
|
|
| 31 |
-By default, all top genes will be labeled.} |
|
| 28 |
+\item{featureDisplay}{A character string for the \code{rowData} variable name
|
|
| 29 |
+to indicate what type of feature ID should be displayed. If set by |
|
| 30 |
+\code{\link{setSCTKDisplayRow}}, will by default use it. If \code{NULL}, will
|
|
| 31 |
+use \code{rownames(inSCE)}.}
|
|
| 32 | 32 |
} |
| 33 | 33 |
\value{
|
| 34 |
-plot object |
|
| 34 |
+ggplot of HVG metrics |
|
| 35 | 35 |
} |
| 36 | 36 |
\description{
|
| 37 | 37 |
Plot highly variable genes |
| 38 | 38 |
} |
| 39 | 39 |
\examples{
|
| 40 | 40 |
data("mouseBrainSubsetSCE", package = "singleCellTK")
|
| 41 |
-mouseBrainSubsetSCE <- scranModelGeneVar(mouseBrainSubsetSCE, "logcounts") |
|
| 42 |
-plotTopHVG(mouseBrainSubsetSCE, method = "modelGeneVar", |
|
| 43 |
- n = 1000, labelsCount = 0) |
|
| 41 |
+mouseBrainSubsetSCE <- runModelGeneVar(mouseBrainSubsetSCE) |
|
| 42 |
+plotTopHVG(mouseBrainSubsetSCE, method = "modelGeneVar") |
|
| 43 |
+} |
|
| 44 |
+\seealso{
|
|
| 45 |
+\code{\link{runFeatureSelection}}, \code{\link{runSeuratFindHVG}},
|
|
| 46 |
+\code{\link{runModelGeneVar}}, \code{\link{getTopHVG}}
|
|
| 44 | 47 |
} |
Yichen Wang authored on 10/05/2021 22:58:10
| ... | ... |
@@ -4,7 +4,13 @@ |
| 4 | 4 |
\alias{plotTopHVG}
|
| 5 | 5 |
\title{Plot highly variable genes}
|
| 6 | 6 |
\usage{
|
| 7 |
-plotTopHVG(inSCE, method = "vst", hvgList = NULL, n = NULL, labelsCount = NULL) |
|
| 7 |
+plotTopHVG( |
|
| 8 |
+ inSCE, |
|
| 9 |
+ method = c("vst", "mean.var.plot", "dispersion", "modelGeneVar"),
|
|
| 10 |
+ hvgList = NULL, |
|
| 11 |
+ n = NULL, |
|
| 12 |
+ labelsCount = NULL |
|
| 13 |
+) |
|
| 8 | 14 |
} |
| 9 | 15 |
\arguments{
|
| 10 | 16 |
\item{inSCE}{Input \code{SingleCellExperiment} object containing the
|
| ... | ... |
@@ -30,3 +36,9 @@ plot object |
| 30 | 36 |
\description{
|
| 31 | 37 |
Plot highly variable genes |
| 32 | 38 |
} |
| 39 |
+\examples{
|
|
| 40 |
+data("mouseBrainSubsetSCE", package = "singleCellTK")
|
|
| 41 |
+mouseBrainSubsetSCE <- scranModelGeneVar(mouseBrainSubsetSCE, "logcounts") |
|
| 42 |
+plotTopHVG(mouseBrainSubsetSCE, method = "modelGeneVar", |
|
| 43 |
+ n = 1000, labelsCount = 0) |
|
| 44 |
+} |
Yichen Wang authored on 05/05/2021 21:27:43
| ... | ... |
@@ -7,15 +7,19 @@ |
| 7 | 7 |
plotTopHVG(inSCE, method = "vst", hvgList = NULL, n = NULL, labelsCount = NULL) |
| 8 | 8 |
} |
| 9 | 9 |
\arguments{
|
| 10 |
-\item{inSCE}{Input \code{SingleCellExperiment} object containing the computations.}
|
|
| 10 |
+\item{inSCE}{Input \code{SingleCellExperiment} object containing the
|
|
| 11 |
+computations.} |
|
| 11 | 12 |
|
| 12 |
-\item{method}{Select either "vst", "mean.var.plot", "dispersion" or "modelGeneVar".}
|
|
| 13 |
+\item{method}{Select either "vst", "mean.var.plot", "dispersion" or
|
|
| 14 |
+"modelGeneVar".} |
|
| 13 | 15 |
|
| 14 |
-\item{hvgList}{Character vector indicating the labels of highly variable genes.}
|
|
| 16 |
+\item{hvgList}{Character vector indicating the labels of highly variable
|
|
| 17 |
+genes.} |
|
| 15 | 18 |
|
| 16 |
-\item{n}{Specify the number of top genes to highlight in red. If `hvgList`
|
|
| 17 |
-parameter is not provided, this parameter can be used simply to specify |
|
| 18 |
-the number of top genes to highlight in red.} |
|
| 19 |
+\item{n}{Specify the number of top genes to highlight in red. If
|
|
| 20 |
+\code{hvgList}
|
|
| 21 |
+ parameter is not provided, this parameter can be used simply to specify |
|
| 22 |
+ the number of top genes to highlight in red.} |
|
| 19 | 23 |
|
| 20 | 24 |
\item{labelsCount}{Specify the number of data points/genes to label.
|
| 21 | 25 |
By default, all top genes will be labeled.} |
Irzam Sarfraz authored on 21/03/2021 07:24:34
| ... | ... |
@@ -4,7 +4,7 @@ |
| 4 | 4 |
\alias{plotTopHVG}
|
| 5 | 5 |
\title{Plot highly variable genes}
|
| 6 | 6 |
\usage{
|
| 7 |
-plotTopHVG(inSCE, method = "vst", hvgList) |
|
| 7 |
+plotTopHVG(inSCE, method = "vst", hvgList = NULL, n = NULL, labelsCount = NULL) |
|
| 8 | 8 |
} |
| 9 | 9 |
\arguments{
|
| 10 | 10 |
\item{inSCE}{Input \code{SingleCellExperiment} object containing the computations.}
|
| ... | ... |
@@ -12,6 +12,13 @@ plotTopHVG(inSCE, method = "vst", hvgList) |
| 12 | 12 |
\item{method}{Select either "vst", "mean.var.plot", "dispersion" or "modelGeneVar".}
|
| 13 | 13 |
|
| 14 | 14 |
\item{hvgList}{Character vector indicating the labels of highly variable genes.}
|
| 15 |
+ |
|
| 16 |
+\item{n}{Specify the number of top genes to highlight in red. If `hvgList`
|
|
| 17 |
+parameter is not provided, this parameter can be used simply to specify |
|
| 18 |
+the number of top genes to highlight in red.} |
|
| 19 |
+ |
|
| 20 |
+\item{labelsCount}{Specify the number of data points/genes to label.
|
|
| 21 |
+By default, all top genes will be labeled.} |
|
| 15 | 22 |
} |
| 16 | 23 |
\value{
|
| 17 | 24 |
plot object |
Irzam Sarfraz authored on 04/11/2020 16:29:49
| 1 | 1 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,21 @@ |
| 1 |
+% Generated by roxygen2: do not edit by hand |
|
| 2 |
+% Please edit documentation in R/plotTopHVG.R |
|
| 3 |
+\name{plotTopHVG}
|
|
| 4 |
+\alias{plotTopHVG}
|
|
| 5 |
+\title{Plot highly variable genes}
|
|
| 6 |
+\usage{
|
|
| 7 |
+plotTopHVG(inSCE, method = "vst", hvgList) |
|
| 8 |
+} |
|
| 9 |
+\arguments{
|
|
| 10 |
+\item{inSCE}{Input \code{SingleCellExperiment} object containing the computations.}
|
|
| 11 |
+ |
|
| 12 |
+\item{method}{Select either "vst", "mean.var.plot", "dispersion" or "modelGeneVar".}
|
|
| 13 |
+ |
|
| 14 |
+\item{hvgList}{Character vector indicating the labels of highly variable genes.}
|
|
| 15 |
+} |
|
| 16 |
+\value{
|
|
| 17 |
+plot object |
|
| 18 |
+} |
|
| 19 |
+\description{
|
|
| 20 |
+Plot highly variable genes |
|
| 21 |
+} |