abundanceContig {scRepertoire} | R Documentation |
This function takes the output of combineTCR(), combineBCR(), or expression2List() and displays the number of clonotypes at specific frequencies by sample or group. Visualization can either be a line graph using calculated numbers or if scale = TRUE, the output will be a density plot. Multiple sequencing runs can be group together using the group parameter. If a matrix output for the data is preferred, set exportTable = TRUE.
abundanceContig( df, cloneCall = "gene+nt", scale = FALSE, group = NULL, exportTable = FALSE )
df |
The product of combineTCR(), combineBCR(), or expression2List(). |
cloneCall |
How to call the clonotype - CDR3 gene (gene), CDR3 nucleotide (nt), CDR3 amino acid (aa), or C DR3 gene+nucleotide (gene+nt). |
scale |
Converts the graphs into denisty plots in order to show relative distributions. |
group |
The column header for which you would like to analyze the data. |
exportTable |
Returns the data frame used for forming the graph to the visualization. |
ggplot of the total or relative adundance of clonotypes across quanta
#Making combined contig data x <- contig_list combined <- combineTCR(x, rep(c("PX", "PY", "PZ"), each=2), rep(c("P", "T"), 3), cells ="T-AB") abundanceContig(combined, cloneCall = "gene", scale = FALSE)