View source: R/VDJ_clonal_expansion_abundances.R
VDJ_clonal_expansion_abundances | R Documentation |
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 )
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. |
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.
## Not run: VDJ_clonal_expansion_abundances(VDJ = small_vgm[[1]], features='VDJ_cgene',count.level='absolute', max.clonotypes=30, rank.clonotypes=T, specific.feat.colors=NULL) ## End(Not run)
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