plotBaselineDensity - 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 ofbaseline
containing primary identifiers. - groupColumn
- name of the column in the
db
slot ofbaseline
containing secondary grouping identifiers. IfNULL
, organize the plot only on values inidColumn
. - colorElement
- one of
c("id", "group")
specifying whether theidColumn
orgroupColumn
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 thecolorElement
column and values being colors. Also controls the order in which values appear on the plot. IfNULL
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. IfNULL
all regions inbaseline
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 ingroupColumn
(“group”) or regions defined in theregions
slot of thebaseline
object (“region”). If this is set to “group”, then the region will behave as thegroupColumn
for purposes of thecolorElement
argument. - style
- type of plot to draw. One of:
"density"
: plots a set of curves for each probability density function inbaseline
, with colors determined by values in thecolorElement
column. Faceting is determined by thefacetBy
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 inid
orcode
. - 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; ifFALSE
draw the plot. - …
- additional arguments to pass to ggplot2::theme.
Value¶
A ggplot object defining the plot.
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))
See also¶
Takes as input a Baseline object returned from groupBaseline.