BarplotOnOff {CellScore} | R Documentation |
This function will generate a horizontal barplot of the OnOff scores of test cell types, as defined by the eset$sub_cell_type1 column of the input dataset. Note that if the cell types as provided in the second argument (score data frame as produced by the function OnOff, are not matching the phenotype of the input dataset, the function will return an error.
BarplotOnOff(eset, group.score)
eset |
an ExpressionSet containing data matrices of normalized expression data, present/absent calls, a gene annotation data.frame and a phenotype data.frame. |
group.score |
a data frame with cell type specific on/off scores as generated by the OnOff function. |
This function returns a list of two objects, as follows:
GroupComparisonsForPlot |
an ordered data.frame of on/off scores, |
OnOffBarplotData |
a data frame of marker gain/loss and aditional features, used for making the plot. |
OnOff
for details on on/off score
calculations, and hgu133plus2CellScore
for details
on the specific expressionSet object that should be provided as an input.
## Load the expression set for the standard cell types library(Biobase) library(hgu133plus2CellScore) # eset.std ## Locate the external data files in the CellScore package rdata.path <- system.file("extdata", "eset48.RData", package = "CellScore") tsvdata.path <- system.file("extdata", "cell_change_test.tsv", package = "CellScore") if (file.exists(rdata.path) && file.exists(tsvdata.path)) { ## Load the expression set with normalized expressions of 48 test samples load(rdata.path) ## Import the cell change info for the loaded test samples cell.change <- read.delim(file= tsvdata.path, sep="\t", header=TRUE, stringsAsFactors=FALSE) ## Combine the standards and the test data eset <- combine(eset.std, eset48) ## Generate a marker list group.OnOff <- OnOff(eset, cell.change, out.put="marker.list") ## Calculate on/off score for individual samples individ.OnOff <- OnOff(eset, cell.change, out.put="individual") ## Plot pyramid bar plot of on/off scores BarplotOnOff(eset, group.OnOff$scores) }