MARVEL (version 1.4.0)

PlotValues: Plot percent spliced-in (PSI) or gene expression values

Description

Plots percent spliced-in (PSI) or gene expression values across different groups of cells. This is a wrapper function for PlotValues.Exp and PlotValues.PSI.

Usage

PlotValues(
  MarvelObject,
  cell.group.list,
  feature,
  maintitle = "gene_short_name",
  xlabels.size = 8,
  level,
  min.cells = NULL,
  sigma.sq = 0.001,
  bimodal.adjust = NULL,
  seed = NULL,
  modality.column = "modality.bimodal.adj",
  scale.y.log = FALSE,
  max.cells.jitter = 10000,
  max.cells.jitter.seed = 1,
  cell.group.colors = NULL,
  point.alpha = 0.2
)

Value

An object of class S3 with new slot $adhocPlot$PSI or MarvelObject$adhocPlot$Exp when level set to "splicing" or "gene", respectively.

Arguments

MarvelObject

Marvel object. S3 object generated from TransformExpValues function.

cell.group.list

List of character strings. Each element of the list is a vector of cell IDs corresponding to a cell group. The name of the element will be the cell group label.

feature

Character string. tran_id or gene_id for plotting. Should match tran_id or gene_id column of MarvelObject$ValidatedSpliceFeature or MarvelObject$GeneFeature slot when level set to "splicing" or "gene", respectively.

maintitle

Character string. Column to use as plot main title as per MarvelObject$ValidatedSpliceFeature or MarvelObject$GeneFeature when level set to "splicing" or "gene", respectively. Default is "gene_short_name" column.

xlabels.size

Numeric value. Size of x-axis labels as per ggplot2 function. Default is 8.

level

Character string. Indicate "splicing" or "gene" for PSI or gene expression value plotting, respectively.

min.cells

Numeric value. Only applicable when level set to "splicing". The minimum no. of cells expressing the splicing event to be included for analysis.

sigma.sq

Numeric value. Only applicable when level set to "splicing". The variance threshold below which the included/excluded modality will be defined as primary sub-modality, and above which it will be defined as dispersed sub-modality. Please refer to AssignModality function help page for more details. Default is 0.001.

bimodal.adjust

Logical. Only applicable when level set to "splicing". When set to TRUE, MARVEL will identify false bimodal modalities and reassign them as included/excluded modality. Please refer to AssignModality function help page for more details.

seed

Numeric value. Only applicable when level set to "splicing". Ensure the fitdist function returns the same values for alpha and beta paramters each time this function is executed using the same random number generator. Please refer to AssignModality function help page for more details.

modality.column

Character string. Only applicable when level set to "splicing". Can take the value "modality", "modality.var" or "modality.bimodal.adj". Please refer to AssignModality function help page for more details. Default is "modality.bimodal.adj".

scale.y.log

Logical value. Only applicable when level set to "splicing". If set to TRUE, the y-axis of will log10-scaled. Useful when most PSI values are extremely small (< 0.02) or big (> 0.98). Default is FALSE.

max.cells.jitter

Numeric value. Only applicable when level set to "splicing". Maximum number of cells for jitter points. Cells are randomly downsampled to show on jitter plot. Useful when there are large number of cells so that individual jitter points do not overcrowd the violin plot. Specified together with max.cells.jitter.seed. To disable this option, specify a value large than the number of cells in each cell group.

max.cells.jitter.seed

Numeric value. Only applicable when level set to "splicing". Cells downsampled are reproducible. Specified together with max.cells.jitter.

cell.group.colors

Character string. Vector of colors for the cell groups specified for PCA analysis using cell.type.columns, cell.type.variable, and cell.type.labels. If not specified, default ggplot2 colors will be used.

point.alpha

Numeric value. Transparency of the data points. Takes any values between 0-1. Default value is 0.2.

Examples

marvel.demo <- readRDS(system.file("extdata/data", "marvel.demo.rds", package="MARVEL"))

# Define cell groups to plot
df.pheno <- marvel.demo$SplicePheno
cell.group.g1 <- df.pheno[which(df.pheno$cell.type=="iPSC"), "sample.id"]
cell.group.g2 <- df.pheno[which(df.pheno$cell.type=="Endoderm"), "sample.id"]
cell.group.list <- list(cell.group.g1, cell.group.g2)
names(cell.group.list) <- c("iPSC", "Endoderm")

# Plot
marvel.demo <- PlotValues(MarvelObject=marvel.demo,
                          cell.group.list=cell.group.list,
                          feature="chr17:8383254:8382781|8383157:-@chr17:8382143:8382315",
                          level="splicing",
                          min.cells=5,
                          xlabels.size=5
                          )

# Check output
marvel.demo$adhocPlot$PSI