plotTissueDist: plot Startrac.dist (tissue distribution preference)

In Japrin/STARTRAC: Single T-cell Analysis by Rna-seq and Tcr TRACking

plot Startrac.dist (tissue distribution preference)

Description

plot Startrac.dist (tissue distribution preference)

Usage

plotTissueDist(
  OR.mtx,
  k = 2,
  method.distance = "cosine",
  do.hclust = T,
  out.prefix = NULL,
  OR.max = 3,
  OR.min = 0,
  col.rid = "rid",
  col.ht = circlize::colorRamp2(c(0, 1, 3), viridis::viridis(3)),
  exp.name = expression(italic(OR)),
  p.tb = NULL,
  charSig.tb = NULL,
  pdf.width = 5.5,
  pdf.height = 10,
  ...
)

Arguments

OR.mtx	matrix. OR data
k	integer. for row-clustering. (default: 2)
method.distance	character. for row-clustering. (default: "cosine")
do.hclust	logical. for row-clustering. (default: TRUE)
out.prefix	character. out.prefix (default: NULL)
OR.max	double. maximum of OR. ORs > this value will be set to this value (default: 3)
OR.min	double. minimum of OR. ORs < this value will be set to this value (default: 0)
col.rid	character. column indicating row ID (default: "rid")
col.ht	vector;
exp.name	character. legend title (default: expression(italic(OR))
p.tb	data.table. p.value table. A column indicated by col.rid is required. (default: NULL)
charSig.tb	data.table. charSig table. A column indicated by col.rid is required. (default: NULL)
pdf.width	double. pdf width (default: 5.5)
pdf.height	double. pdf height (default: 10)
...	parameters passed to sscVis:::plotMatrix.simple().

Details

plot Startrac.dist (tissue distribution preference).

Value

object returned by sscVis:::plotMatrix.simple()

Japrin/STARTRAC documentation built on Dec. 4, 2023, 1:35 a.m.