Plots a logoplot of the CDR3 aminoacid region
VDJ_logoplot_vector(cdr3.vector, length_cdr3, seq_type)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"
Value
Returns the logo plot.
Examples
VDJ_logoplot_vector(
cdr3.vector = Platypus::small_vgm[[1]]$VDJ_cdr3s_aa
,length_cdr3 = "auto",seq_type = "auto")
#> Returning logoplot based on 5 sequences of a total 34 input sequences
