generateKirchenplot: Plotting a Kirchenplot

In genBaRcode: Analysis and Visualization Tools for Genetic Barcode Data

Plotting a Kirchenplot

Description

Generates a barplot based on read counts. If ori_BCs is provided the bar color reflects the distance between a particular barcode to one of the provided barcode sequences.

Usage

generateKirchenplot(
  BC_dat,
  ori_BCs = NULL,
  ori_BCs2 = NULL,
  loga = TRUE,
  col_type = NULL,
  m = "hamming",
  setLabels = c("BC-Set 1", "Rest", "BC-Set 2")
)

Arguments

BC_dat	a BCdat object.
ori_BCs	a vector of character strings containing known barcode sequences (without the fixed positions of the barcode construct).
ori_BCs2	a vector of character strings containing a 2nd set of known barcode sequences (also without the fixed positions).
loga	a logical value, indicating the use or non-use of logarithmic read count values.
col_type	character string, choosing one of the availabe color palettes ("rainbow", "heat.colors", "topo.colors", "greens", "wild" - see package "grDevices")
m	a character string, Method for distance calculation, default value is Hamming distance. Possible values are "osa", "lv", "dl", "hamming", "lcs", "qgram", "cosine", "jaccard", "jw", "soundex" (see stringdist function of the stringdist-package for more information). If neither 'ori_BCs' nor 'ori_BCs2' are provided with input the choice of 'm' does not matter.
setLabels	a character vector, containing three strings serving as plot labels.

Value

a ggplot2 object

genBaRcode documentation built on March 31, 2023, 11:02 p.m.