yingxinlin authored on 12/04/2020 16:17:45
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@@ -46,8 +46,8 @@ A function to visualise the features distribtuion for |
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a list of SingleCellExperiment |
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} |
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\examples{
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-data(sce_control_subset) |
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-data(sce_ctcl_subset) |
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+data(sce_control_subset, package = "CiteFuse") |
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+data(sce_ctcl_subset, package = "CiteFuse") |
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visualiseExprsList(sce_list = list(control = sce_control_subset, |
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ctcl = sce_ctcl_subset), |
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plot = "boxplot", |
yingxinlin authored on 12/04/2020 15:42:00
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@@ -46,8 +46,8 @@ A function to visualise the features distribtuion for |
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a list of SingleCellExperiment |
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} |
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\examples{
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-data("sce_control_subset", package = "CiteFuse")
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-data("sce_ctcl_subset", package = "CiteFuse")
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+data(sce_control_subset) |
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+data(sce_ctcl_subset) |
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visualiseExprsList(sce_list = list(control = sce_control_subset, |
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ctcl = sce_ctcl_subset), |
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plot = "boxplot", |
yingxinlin authored on 11/03/2020 08:01:00
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new file mode 100644 |
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@@ -0,0 +1,60 @@ |
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+% Generated by roxygen2: do not edit by hand |
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+% Please edit documentation in R/visualise_features.R |
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+\name{visualiseExprsList}
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+\alias{visualiseExprsList}
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+\title{visualiseExprsList}
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+\usage{
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+visualiseExprsList( |
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+ sce_list, |
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+ plot = c("boxplot", "violin", "jitter", "density"),
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+ altExp_name = "none", |
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+ exprs_value = "logcounts", |
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+ group_by = NULL, |
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+ feature_subset = NULL, |
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+ cell_subset = NULL, |
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+ n = NULL |
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+) |
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+} |
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+\arguments{
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+\item{sce_list}{A list of SingleCellExperiment object}
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+ |
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+\item{plot}{Type of plot, includes boxplot, violin, jitter, density,
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+and pairwise. By default is boxplot} |
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+ |
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+\item{altExp_name}{A character indicates which expression matrix is used.
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+by default is none (i.e. RNA).} |
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+ |
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+\item{exprs_value}{A character indicates which expression value
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+in assayNames is used.} |
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+ |
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+\item{group_by}{A character indicates how is the expression
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+will be group in the plots (stored in colData).} |
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+ |
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+\item{feature_subset}{A vector of characters indicates
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+the subset of features that are used for visualisation} |
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+ |
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+\item{cell_subset}{A vector of characters indicates
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+the subset of cells that are used for visualisation} |
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+ |
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+\item{n}{A numeric indicates the top expressed features to show.}
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+} |
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+\value{
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+A ggplot to visualise te features distribution |
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+} |
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+\description{
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+A function to visualise the features distribtuion for |
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+a list of SingleCellExperiment |
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+} |
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+\examples{
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+data("sce_control_subset", package = "CiteFuse")
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+data("sce_ctcl_subset", package = "CiteFuse")
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+visualiseExprsList(sce_list = list(control = sce_control_subset, |
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+ctcl = sce_ctcl_subset), |
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+plot = "boxplot", |
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+altExp_name = "none", |
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+exprs_value = "logcounts", |
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+feature_subset = c("hg19_CD8A"),
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+group_by = c("SNF_W_louvain", "SNF_W_louvain"))
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+ |
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+ |
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+} |