APackOfTheClones
Visualization of Clonal Expansion for Single Cell Immune Profiles

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388
Source code
56
Man pages
21
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APackOfTheClones: Visualization of Clonal Expansion for Single Cell Immune Profiles
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API

API for APackOfTheClones
Visualization of Clonal Expansion for Single Cell Immune Profiles

Global functions
.convertClonecall Source code
.onAttach Source code
.theCall Source code
APOTCPlot Man page Source code
APOTCPlot_error_handler Source code
APackOfTheClones Man page
APackOfTheClones-package Man page
AdjustAPOTC Man page Source code
AdjustAPOTC_error_handler Source code
ApotcData Source code
ApotcGGPlot Source code
RunAPOTC Man page Source code
RunAPOTC_parameter_checker Source code
RunAPOTC_partial_arg_checker Source code
add Source code
addIdentsLabelsColors Source code
addInitialCentroids Source code
addRawClusteredCloneSizes Source code
add_blend_link_colors Source code
add_default_theme Source code
add_legend_backing Source code
add_link_colors Source code
add_plain_link_colors Source code
aggregate_clone_sizes Source code
any_reduction_exists Source code
apotc_aes_string Source code
apotc_highlight_clones_error_handler Source code
apotc_rename_aes Source code
applyListAsArgsTo Source code
as_expression Source code
as_table Source code
attempt_correction Source code
bound_num Source code
calculate_legend_spacing Source code
calculate_repulsion_vectors Source code
calculate_transformation_vectors Source code
change_clone_scale Source code
change_rad_scale Source code
check_apotc_identifiers Source code
check_coord_args Source code
check_filtering_conditions Source code
check_is_apotc_ggplot Source code
check_is_list_and_elements Source code
check_legend_params Source code
check_repulsion_params Source code
circlepackClones Source code
clonal_expansion_plot Man page Source code
closest_word Source code
col_cond_vec_to_filter_str Source code
col_conds_to_str_w_insert Source code
combined_pbmc Man page
compute_line_link_df Source code
construct_prefix_vector Source code
containsAnyApotcData Source code
containsApotcRun Man page Source code
contains_clonotypes Source code
contains_duplicates Source code
convert_list_var_str_to_char Source code
convert_named_numeric_to_table Source code
convert_table_to_named_numeric Source code
convert_to_dataframe Source code
convert_to_rad_decrease Source code
convert_to_string_if_expr Source code
correct_legend_coord_if_str Source code
countCloneSizes Man page Source code
countCloneSizes_arg_checker Source code
count_clone_sizes Man page Source code
count_clones Source code
count_raw_clone_sizes Source code
cpp_circle_layout Source code
create_empty_int_hash Source code
create_empty_table Source code
create_err_msg Source code
create_hash_from_keys Source code
create_initial_apotc_plot Source code
create_mutator Source code
create_valueless_vector_hash Source code
deleteApotcData Man page Source code
deparse_object_id Source code
deprecation_docstring Source code
df_full_join Source code
divide Source code
do_cl_intersect Source code
do_cluster_intersect Source code
do_proceed Source code
end_progress_bar Source code
ensure_proper_table Source code
enumerate Source code
estimate_best_legend_df Source code
estimate_clone_scale_factor Source code
estimate_legend_sizes Source code
estimate_link_alpha Source code
estimate_link_width Source code
estimate_top_left_circ_coord Source code
extract_and_add_colors Source code
filter_clonesize_2way_if_need Source code
filter_publicity Source code
filter_shared_if_needed Source code
filter_shared_that_contain Source code
filter_top_by_cluster Source code
filter_top_clones Source code
filter_top_clonesize Source code
filter_top_shared Source code
filter_top_shared_per_cl Source code
filter_top_shared_w_clone_table Source code
filter_top_sizes_if_needed Source code
find_centroids Source code
find_seurat_command Source code
gen_clone_color_vector Source code
gen_cluster_color_hashmap Source code
gen_labels Source code
gen_unpositioned_legend_df Source code
generate_legend_df Source code
getApotcData Source code
getApotcDataIds Man page Source code
getApotcDataIfExistsElseCreate Source code
getElementDiff Source code
getLastApotcData Source code
getLastApotcDataId Man page Source code
getReductionCentroids Man page Source code
getSharedClones Man page Source code
getSharedClones_error_handler Source code
get_2d_embedding Source code
get_aggregated_clone_sizes Source code
get_apotc_plot_dims Source code
get_apotc_plot_dims_from_df Source code
get_apotcdata Source code
get_at_index Source code
get_average_hex Source code
get_average_vector Source code
get_centroid_x Source code
get_centroid_y Source code
get_centroids Source code
get_circle_x Source code
get_clone_scale_factor Source code
get_clonecall Source code
get_clonotypes Source code
get_cluster_centroids Source code
get_cluster_colors Source code
get_clusterlists Source code
get_command_name Source code
get_component_repulsion_vector Source code
get_curr_reduc_names Source code
get_default_apotc_id Source code
get_err_type_str Source code
get_error_strings Source code
get_estimated_legend_sizes Source code
get_first_char Source code
get_first_legend_layer_index Source code
get_first_nonempty Source code
get_ggplot_data Source code
get_ident_index Source code
get_ident_levels Source code
get_idents Source code
get_label_coords Source code
get_label_x Source code
get_labels Source code
get_last_legend_layer_index Source code
get_layers_after_legend Source code
get_legend_backing_minmax_dims Source code
get_legend_dims Source code
get_legend_layer_indices Source code
get_legend_title_coord Source code
get_metadata_filter_string Source code
get_num_clones Source code Source code
get_num_clusters Source code
get_num_total_clusters Source code
get_parent_func_args Source code
get_parent_params Source code
get_plot_dims Source code
get_plottable_df_with_color Source code
get_processed_argnames Source code
get_processed_clone_sizes Source code
get_processed_legend_sizes Source code
get_rad_decrease Source code
get_rad_scale_factor Source code
get_raw_clone_sizes Source code
get_raw_shared_clones Source code
get_reduction_base Source code
get_repulsed_clusterlists Source code
get_retain_scale_dims Source code
get_right_of_dollarsign Source code
get_shared_clones Source code
get_top_clonotypes Source code
get_unique_clonotypes Source code
get_unique_pairs_up_to Source code
get_unique_table_values Source code
get_unpositioned_y_coords Source code
get_valid_num_clusters Source code
get_xr Source code
get_yr Source code
getlast Source code
gg_color_hue Source code
has_layers_after_legend Source code
has_legend Source code
hash_from_tablelist Source code
haveSameElements Source code
have_default_idents Source code
id_segment_to_varargs_list Source code
ident_into_seurat_clusters Source code
if_a_logical_convert_null Source code
ind Source code
infer_object_id_if_needed Source code
init_empty_table_list Source code
init_list Source code
init_numeric Source code
initializeApotcData Source code
initialize_direction_vectors Source code
initialize_list_of_transformation_vectors Source code
insert_colors Source code
insert_labels Source code
insert_legend Source code
integrate_tcr Man page Source code
intersect_common_table_lists Source code
intersect_common_tables Source code
isApotcGGPlot Source code
isValidClusterList Source code
isValidListOfClusterLists Source code
is_a_character Source code
is_a_logical Source code
is_a_numeric Source code
is_a_numeric_in_0_1 Source code
is_a_positive_integer Source code
is_a_positive_numeric Source code
is_an_integer Source code
is_bound_between Source code
is_empty Source code
is_even Source code
is_false Source code
is_int Source code
is_integer Source code
is_integer_pair Source code
is_list_of_empty_tables Source code
is_list_of_numeric_pair Source code
is_numeric_pair Source code
is_odd Source code
is_output_of_countCloneSizes Source code
is_output_of_getSharedClones Source code
is_pair Source code
is_positive_integer Source code
is_positive_numeric Source code
is_seurat_object Source code
is_undetailed Source code
is_valid_args Source code
is_valid_cluster Source code
is_valid_filter_str Source code
is_valid_nonempty_cluster Source code
is_vector Source code
is_vowel Source code
isnt_empty Source code
isnt_empty_nor_na Source code
isnt_na Source code
join_error_strings Source code
join_list_of_characters Source code
lapply_clusterlists Source code
lengthcheck Source code
lengthcheck_coord_args Source code
lengthcheck_ifnotnull Source code
log_seurat_command Source code
makeGetter Source code
makeSetter Source code
make_apotc_command Source code
make_undetailed_df Source code
match_clonotypes_to_sizes Source code
match_index Source code
max_rad Source code
max_y Source code
md_deprecation_docstring Source code
mergeCloneSizes Man page Source code
min_rad Source code
min_y Source code
move_cluster Source code
move_coord_list_by_same_amount Source code
move_unpositioned_legend_df Source code
multiply Source code
name_latest_layer Source code
name_latest_legend_layer Source code
nudge_clusters Source code
nudge_labels Source code
num_circles_covered_by_legend Source code
operate_on_label_locations Source code
operate_on_same_length_lists Source code
overlayLegend Man page Source code
overlayLegend_error_handler Source code
overlay_line_links Source code
overlay_links Source code
overlay_shared_clone_links Source code
pack_into_clusterlists Source code
pair_colors_to_hash Source code
parse_to_metadata_filter_str Source code
parse_to_object_id Source code
plot_clusters Source code
prepend_indefinite_article Source code
print_completion_time Source code
process_argnames Source code
process_legend_spacing Source code
process_link_alpha Source code
process_link_width Source code
process_rad_vec Source code
rcppConstructLineLinkDf Source code
rcppFilterReductionCoords Source code
rcppGetEdgeCircleindices Source code
rcppGetUniquePairsUpTo Source code
rcppRemoveUniqueClonesHelper Source code
rcppRescaleClones Source code
rcppUnionListOfNamedNumericsHelper Source code
read_centroids Source code
recolor_clusters Source code
relocate_clusters Source code
relocate_labels Source code
removeLegend Man page Source code
remove_ggplot_layers Source code
remove_legend_and_layers_after Source code
remove_unique_clones_if Source code
renameApotcRun Man page Source code
rename_labels Source code
repr_as_string Source code
repulseClusters Source code
repulse_cluster Source code
scale_hex_brightness Source code
secretly_init_name Source code
select_cols Source code
setApotcData Source code
setModifiedClusterlists Source code
set_clone_scale_factor Source code
set_cluster_colors Source code
set_clusterlists Source code
set_ggplot_data Source code
set_idents Source code
set_labels Source code
set_meta_ident_col Source code
set_metadata_filter_string Source code
set_raw_clone_sizes Source code
seurat_extractfield Source code
should_change Source code
should_compute Source code
should_estimate Source code
showCloneHighlight Man page Source code
sort_and_join_conds_by_and Source code
sort_each_clone_size_table Source code
sort_each_table Source code
sort_if_desc_arg_not_null Source code
sort_if_needed Source code
start_progress_bar Source code
starts_with_vowel Source code
strip_and_lower Source code
strip_spaces Source code
strip_to_numeric Source code
strip_unquoted_spaces Source code
subsetSeuratMetaData Source code
subset_dataframe Source code
subset_to_only_edge_circles Source code
subtract Source code
to_string_rep_with_insert Source code
trans_coord Source code
typecheck Source code
union_list_of_named_numerics Source code
union_list_of_tables Source code
unname_if Source code
unname_if_empty Source code
update_clusterlist_df Source code
user_attempt_correction Source code
user_get_reduc_obj Source code
val Source code
val1 Source code
varargs_list_to_id_segment Source code
vizAPOTC Man page Source code
zip Source code
APackOfTheClones documentation built on Oct. 11, 2024, 1:08 a.m.

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