1. singleCellTK
  2. man
  3. plotScanpyMarkerGenesViolin.Rd
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Bugs fixes in Scanpy

npervaiz authored on 02/01/2023 19:12:26
Showing 1 changed files
man/plotScanpyMarkerGenesViolin.Rd
History View file @ 6987800d
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@@ -27,10 +27,10 @@ plotScanpyMarkerGenesViolin
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 data(scExample, package = "singleCellTK")
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 \dontrun{
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 sce <- runScanpyNormalizeData(sce, useAssay = "counts")
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+sce <- runScanpyFindHVG(sce, useAssay = "scanpyNormData", method = "seurat")
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 sce <- runScanpyScaleData(sce, useAssay = "scanpyNormData")
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-sce <- runScanpyFindHVG(sce, useAssay = "scanpyScaledData", method = "seurat")
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-sce <- runScanpyPCA(sce, useAssay = "scanpyNormData")
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-sce <- runScanpyFindClusters(sce, useAssay = "counts")
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+sce <- runScanpyPCA(sce, useAssay = "scanpyScaledData")
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+sce <- runScanpyFindClusters(sce, useReducedDim = "scanpyPCA")
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 sce <- runScanpyFindMarkers(sce, colDataName = "Scanpy_louvain_1" )
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 plotScanpyMarkerGenesViolin(sce, groups = '0')
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 }
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Minor edits to scanpy functions

npervaiz authored on 22/12/2022 12:16:44
Showing 1 changed files
man/plotScanpyMarkerGenesViolin.Rd
History View file @ 9d91028a
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@@ -27,6 +27,8 @@ plotScanpyMarkerGenesViolin
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 data(scExample, package = "singleCellTK")
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 \dontrun{
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 sce <- runScanpyNormalizeData(sce, useAssay = "counts")
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+sce <- runScanpyScaleData(sce, useAssay = "scanpyNormData")
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+sce <- runScanpyFindHVG(sce, useAssay = "scanpyScaledData", method = "seurat")
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 sce <- runScanpyPCA(sce, useAssay = "scanpyNormData")
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 sce <- runScanpyFindClusters(sce, useAssay = "counts")
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 sce <- runScanpyFindMarkers(sce, colDataName = "Scanpy_louvain_1" )
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bug fixes

feature parameter added to plots

npervaiz authored on 03/11/2022 15:58:29
Showing 1 changed files
man/plotScanpyMarkerGenesViolin.Rd
History View file @ 1a2c8f0c
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@@ -4,7 +4,7 @@
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 \alias{plotScanpyMarkerGenesViolin}
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 \title{plotScanpyMarkerGenesViolin}
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 \usage{
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-plotScanpyMarkerGenesViolin(inSCE, groups = NULL, nGenes = 10)
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+plotScanpyMarkerGenesViolin(inSCE, groups = NULL, features = NULL, nGenes = 10)
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 }
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 \arguments{
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 \item{inSCE}{Input \code{SingleCellExperiment} object.}
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@@ -12,6 +12,9 @@ plotScanpyMarkerGenesViolin(inSCE, groups = NULL, nGenes = 10)
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 \item{groups}{The groups for which to show the gene ranking. Default \code{NULL}
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 means that all groups will be considered.}
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+\item{features}{List of genes to plot. Is only useful if interested in a
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+custom gene list}
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+
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 \item{nGenes}{Number of genes to show. Default \code{10}}
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 }
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 \value{
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Bug fixes and documentation

npervaiz authored on 02/11/2022 12:13:26
Showing 1 changed files
man/plotScanpyMarkerGenesViolin.Rd
History View file @ 4f02e9c2
... ... 
@@ -26,7 +26,7 @@ data(scExample, package = "singleCellTK")
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 sce <- runScanpyNormalizeData(sce, useAssay = "counts")
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 sce <- runScanpyPCA(sce, useAssay = "scanpyNormData")
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 sce <- runScanpyFindClusters(sce, useAssay = "counts")
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-sce <- runScanpyFindMarkers(sce, colDataName = "Scanpy_louvain" )
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+sce <- runScanpyFindMarkers(sce, colDataName = "Scanpy_louvain_1" )
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 plotScanpyMarkerGenesViolin(sce, groups = '0')
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 }
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 }
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Scanpy wrapper functions

npervaiz authored on 12/10/2022 14:09:33
Showing 1 changed files
man/plotScanpyMarkerGenesViolin.Rd
History View file @ aa5d89a1
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new file mode 100644
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@@ -0,0 +1,32 @@
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/scanpyFunctions.R
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+\name{plotScanpyMarkerGenesViolin}
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+\alias{plotScanpyMarkerGenesViolin}
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+\title{plotScanpyMarkerGenesViolin}
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+\usage{
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+plotScanpyMarkerGenesViolin(inSCE, groups = NULL, nGenes = 10)
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+}
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+\arguments{
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+\item{inSCE}{Input \code{SingleCellExperiment} object.}
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+
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+\item{groups}{The groups for which to show the gene ranking. Default \code{NULL}
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+means that all groups will be considered.}
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+
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+\item{nGenes}{Number of genes to show. Default \code{10}}
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+}
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+\value{
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+plot object
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+}
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+\description{
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+plotScanpyMarkerGenesViolin
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+}
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+\examples{
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+data(scExample, package = "singleCellTK")
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+\dontrun{
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+sce <- runScanpyNormalizeData(sce, useAssay = "counts")
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+sce <- runScanpyPCA(sce, useAssay = "scanpyNormData")
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+sce <- runScanpyFindClusters(sce, useAssay = "counts")
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+sce <- runScanpyFindMarkers(sce, colDataName = "Scanpy_louvain" )
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+plotScanpyMarkerGenesViolin(sce, groups = '0')
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+}
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+}