plotBaselineDensity: Plots BASELINe probability density functions

In shazam: Immunoglobulin Somatic Hypermutation Analysis

Plots BASELINe probability density functions

Description

plotBaselineDensity plots the probability density functions resulting from selection analysis using the BASELINe method.

Usage

plotBaselineDensity(
  baseline,
  idColumn,
  groupColumn = NULL,
  colorElement = c("id", "group"),
  colorValues = NULL,
  title = NULL,
  subsetRegions = NULL,
  sigmaLimits = c(-5, 5),
  facetBy = c("region", "group"),
  style = c("density"),
  sizeElement = c("none", "id", "group"),
  size = 1,
  silent = FALSE,
  ...
)

Arguments

baseline	Baseline object containing selection probability density functions.
idColumn	name of the column in the db slot of baseline containing primary identifiers.
groupColumn	name of the column in the db slot of baseline containing secondary grouping identifiers. If NULL, organize the plot only on values in idColumn.
colorElement	one of c("id", "group") specifying whether the idColumn or groupColumn will be used for color coding. The other entry, if present, will be coded by line style.
colorValues	named vector of colors for entries in colorElement, with names defining unique values in the colorElement column and values being colors. Also controls the order in which values appear on the plot. If NULL alphabetical ordering and a default color palette will be used.
title	string defining the plot title.
subsetRegions	character vector defining a subset of regions to plot, correspoding to the regions for which the baseline data was calculated. If NULL all regions in baseline are plotted.
sigmaLimits	numeric vector containing two values defining the c(lower, upper) bounds of the selection scores to plot.
facetBy	one of c("region", "group") specifying which category to facet the plot by, either values in groupColumn ("group") or regions defined in the regions slot of the baseline object ("region"). If this is set to "group", then the region will behave as the groupColumn for purposes of the colorElement argument.
style	type of plot to draw. One of: "density": plots a set of curves for each probability density function in baseline, with colors determined by values in the colorElement column. Faceting is determined by the facetBy argument.
sizeElement	one of c("none", "id", "group") specifying whether the lines in the plot should be all of the same size (none) or have their sizes depend on the values in id or code.
size	numeric scaling factor for lines, points and text in the plot.
silent	if TRUE do not draw the plot and just return the ggplot2 object; if FALSE draw the plot.
...	additional arguments to pass to ggplot2::theme.

Value

A ggplot object defining the plot.

See Also

Takes as input a Baseline object returned from groupBaseline.

Examples

## Not run: 
# Subset example data as a demo
data(ExampleDb, package="alakazam")
db <- subset(ExampleDb, c_call %in% c("IGHM", "IGHG"))
set.seed(112)
db <- dplyr::slice_sample(db, n=100)

# Collapse clones
db <- collapseClones(db, cloneColumn="clone_id",
                     sequenceColumn="sequence_alignment",
                     germlineColumn="germline_alignment_d_mask",
                     method="thresholdedFreq", minimumFrequency=0.6,
                     includeAmbiguous=FALSE, breakTiesStochastic=FALSE)
                     
# Calculate BASELINe
baseline <- calcBaseline(db, 
                         sequenceColumn="clonal_sequence",
                         germlineColumn="clonal_germline", 
                         testStatistic="focused",
                         regionDefinition=IMGT_V,
                         targetingModel=HH_S5F,
                         nproc=1)
 
# Grouping the PDFs by the sample and isotype annotations
grouped <- groupBaseline(baseline, groupBy=c("sample_id", "c_call"))

# Plot density faceted by region with custom isotype colors
isotype_colors <- c("IGHM"="darkorchid", "IGHD"="firebrick", 
                    "IGHG"="seagreen", "IGHA"="steelblue")
plotBaselineDensity(grouped, "sample_id", "c_call", colorValues=isotype_colors, 
                    colorElement="group", sigmaLimits=c(-1, 1))

# Facet by isotype instead of region
sample_colors <- c("-1h"="steelblue", "+7d"="firebrick")
plotBaselineDensity(grouped, "sample_id", "c_call", facetBy="group",
                    colorValues=sample_colors, sigmaLimits=c(-1, 1))

## End(Not run)

shazam documentation built on Oct. 3, 2023, 1:06 a.m.