VDJ_kmers | R Documentation |
Calculates and plots kmers distributions and frequencies.
VDJ_kmers( VDJ, sequence.column, grouping.column, kmer.k, max.kmers, specific.kmers, plot.format, as.proportions )
VDJ |
VDJ dataframe output from the VDJ_GEX_matrix function. |
sequence.column |
Character vector. One or more sequence column names from the VDJ for kmer counting. if more than one column is provided (e.g. c("VDJ_cdr3s_aa","VJ_cdr3s_aa")) these columns will be pasted together before counting the kmers. |
grouping.column |
Character. Column name of a column to group kmer counting by. This could be "sample_id" to group each kmer by the sample. |
kmer.k |
Integer. Length k of each kmer. |
max.kmers |
Integer. Maximum number of kmers to be plotted in the output barplots. |
specific.kmers |
Character vector. Specific kmers to be plotted in the output barplots. |
plot.format |
Character. The output plot format: 'barplot' for barplots of kmer frequency per group, 'pca' for group-level PCA reduction across the kmer vectors, 'density' for kmer count density plots. |
as.proportions |
Boolean. If TRUE, will return the kmer barplot as proportions instead of absolute counts. |
Returns a ggplot with the kmer analysis depedning on the plot.format parameter
## Not run: #Calculate the 3-kmer frequency for CDRH3s and plot the 20 most abundant kmers. VDJ_kmers(VDJ = Platypus::small_vgm[[1]], ,sequence.columns = c("VDJ_cdr3s_aa"), grouping.column = "sample_id", kmer.k = 3, max.kmers = 20) ## End(Not run)
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