Wrapper function for VDJ_abundances to obtain ranked clonotype barplots

Wraps the VDJ_abundances function and output a barplot of clonotypes ranked by expansion (x axis) with counts of the specific feature values per clonotype (y axis). For a more in-depth configuration of the barplots (e.g., including clonotypes with missing features, different strategies for NA values, etc.), use the VDJ_abundances function with output.format='plots'.

VDJ_clonal_expansion_abundances(
  VDJ,
  features,
  count.level,
  max.clonotypes,
  rank.clonotypes,
  specific.feat.colors
)

Arguments

VDJ

VDJ or VDJ.GEX.matrix[[1]] object, as obtained from the VDJ_GEX_matrix function in Platypus.

features

string or vector of strings, denoting the columns of the VDJ/VDJ.GEX.matrix[[1]] object from which to extract the unique feature values.

count.level

string, 'absolute' will return the absolute counts, 'group.level.proportions' will return the counts divided by the total number or elements/values in the specific groups (group level proportions), 'sample.level.proportions' will return the counts divided by the total number of elements in the sample.

max.clonotypes

integer or NULL, the maximum number of clonotypes for which to count features. If NULL, it will count for all clonotypes.

rank.clonotypes

boolean, if T - clonotypes will be ranked and order according to their expansion.

specific.feat.colors

named list (or NULL) of specific colors to be used in the final barplots.

Value

Either a count dataframe with the following columns: group(=unique group value, e.g., 'clonotype1' if grouping.column='clonotype_id'), sample, group_frequency, unique_feature_values, feature_value_counts, total_feature_names or a barplot of the counts/proportions per feature, per group.

Examples

if (FALSE) {
VDJ_clonal_expansion_abundances(VDJ = small_vgm[[1]],
features='VDJ_cgene',count.level='absolute',
max.clonotypes=30, rank.clonotypes=T, specific.feat.colors=NULL)
}