VDJ_logoplot_vector: Flexible logoplot wrapper

In Platypus: Single-Cell Immune Repertoire and Gene Expression Analysis

Flexible logoplot wrapper

Description

Plots a logoplot of the CDR3 aminoacid region

Usage

VDJ_logoplot_vector(
  cdr3.vector,
  length_cdr3,
  seq_type,
  namespace,
  font,
  method
)

Arguments

cdr3.vector	A character vector of aa sequences. This is to increase flexibility of this function. Such a sequence vector may be retrieved from the VDJ_analyse function output on a clonotype level or from the VDJ_GEX_matrix function output on a per cell level. Additionally, any length of sequence may be used (e.g. HCDR3 only or H and LCDR3 pasted together)
length_cdr3	Integer or character. Defaults to "auto". Sets the length of the CDR3 regions that are selected to be plotted. If set to auto, the most frequently appearing length in the vector will be used
seq_type	passed to ggseqlogo. Can be set to "aa", "dna", "rna" or "other"
namespace	passed to ggseqlogo. Default "auto".
font	passed to ggseqlogo. Default "roboto_medium".
method	passed to ggseqlogo. Default "bits".

Value

Returns the logo plot.

Examples

VDJ_logoplot_vector(
cdr3.vector = Platypus::small_vgm[[1]]$VDJ_cdr3s_aa
,length_cdr3 = "auto",seq_type = "auto")

Platypus documentation built on Oct. 18, 2024, 5:08 p.m.