Package index • vesalius

All functions

add_active_count_tag(): add active count tag

add_active_embedding_tag(): add active embedding tag

add_counts(): Add counts to vesalius assay Adding custom count matrix to a vesalius assay object.

add_embeddings(): Add embeddings Add custom embeddings to vesalius objects

adjust_counts(): adjust count

align_index(): assign coordinates to matched indices

assign_centers(): assign centroid values to active embedding

average_embed(): average image stack between seed and query

back_infer(): Infer normalized counts from shared embedding values

bubble_stack(): importFrom imager nPix

build_mapped_assay(): Build a new vesalius_assay object using mapping information

build_vesalius_assay(): build vesalius assay object

calculate_scale(): calculate scale of assay

cell_type_match(): Compute score based on cell type labels

check_barcodes(): checking overlap between barcodes in counts and coordinates

check_binary_nature(): check binary nature

check_cells(): check if provided cells are contained withing provided territory

check_coordinates(): check if coordinates are of the correct type and format and adjust coordinate value to remove white edge space

check_counts(): check if counts are of the correct type and format

check_deg_method(): check if DEG method is one of the available options

check_dim_selection_method(): check dimension selection method

check_embed_methods(): check if embedding method is present in availble options

check_embedding_selection(): check embedding selection

check_embeddings(): check embeddings checking user provided embedding matrix

check_eq_method(): check if eq method are avilable

check_features(): check features

check_for_zero_counts(): check_for_zero_counts check which barcodes contain all 0 counts and filter

check_group_value(): check if requested territory is in territory list

check_image(): check if image is present

check_image_input(): check image input check if input image is in correct format

check_inputs(): check input checks the validity of input data to build_vesalius_assay

check_isolation_method(): check territory isolation method is available

check_min_spatial_index(): check number of spatial indices present

check_norm(): check if select norm method is an available option

check_norm_methods(): check if norm method is present in availble options

check_segment_trial(): check if segment selection is a valid option

check_segmentation_method(): check if segmentation options are valid for segmentation

check_smoothing_kernel(): check if smoothing method is present in availble options

check_smoothing_level(): check if across level options are valid for smoothing

check_tensor_compression(): check tensor compression

check_territory_trial(): check if territory selection is a valid option

check_tiles(): check tile integretiy

commit_log(): commits function call to log slot

compute_effect_size(): compute_effect_size

compute_nearest_neighbor_graph(): compute and greate nearest neighbor graph

concat_cost(): concat cost - pairwise sum of score complement

concat_embed(): create new embedding from jointly measure spatial omics

concat_matches(): merging batch matches together

convexify(): convexify

vesalius: Spatial coordinates

vesalius: Count matrix for vesalius

create_alpha(): create alpha value if territories need to be highlighted

create_commit_log(): create function log to be commit to the log slot

create_palette(): create color palette from predefine scheme

create_pseudo_centroids(): create centroid vlues for louvain and leiden

create_trial_tag(): create a trail tag name

detect_edges(): detect_edges detect territory edges in black and white images with sobel filter

dispatch_batch(): Dispatch cells into batches

dispatch_cost_groups(): dispatch barcodes to subset cost for match clustering

dispatch_deg_group(): dispatch barcodes to seed and query groups

dispatch_sample(): dispatch barcodes associted with a specific territory in a specific samples

dispatch_territory(): dispatch territories labels territories according to which group they belong to.

distance_pooling(): distance pooling beads of colour segment into seperate territories

ecdf_eq(): internal ecdf eq used for formatting

embed_latent_space(): embed latent space

embed_lsi(): embed lsi

embed_lsi_umap(): embed lsi

embed_nmf(): embed nmf

embed_pca(): embed PCA

embed_pcal(): embed PCA loading values

embed_umap(): embed umap

equalize_image(): equalise image histogram

extend_boundary(): extend image boundary around territory

filter_grid(): filter grid

filter_maps(): filter mapped cells

filter_tiles(): filter tiles

format_c_to_ves(): convert cimg list to vesalius object embedding

format_call(): format function call to list for log update

format_counts_for_deseq2(): format counts for DESeq

format_counts_for_edger(): format counts for edgeR

format_counts_for_logit(): format counts for logistic regression

format_ves_to_c(): convert vesalius_assay to cimg images

future_ves_to_cimg(): convert ves embedding to image

generate_embeddings(): Generate embeddings.

generate_spix(): Generate super pixels from ST

generate_tiles(): generate tiles

get_active_count_tag(): get last count matrix used

get_active_embedding_tag(): get active embedding

get_assay_names(): get assay names from vesalius_assay

get_coordinates(): get coordinates from vesalius_assay

get_cost_contribution(): Compute mapping score contribution to mapping

get_counts(): get counts from vesalius_assay

get_deg_metrics(): get DEG metrics from groups

get_embeddings(): get embeddings from vesalius_assay

get_func_from_commit(): get function name from commit list

get_markers(): get markers from vesalius_assay

get_metric_clusters(): Cluster query cells based on which reference cells they tend to mapped to

get_neighborhood_signal(): Method dispatch function for neighborhood selection

get_signal(): get cell signal from vesalius assays

get_territories(): get territories from vesalius_assay

get_tiles(): get tiles from vesalius_assay

globalise_territories(): globalise territories converts territories number from territory values per segment to territory values overall the entire spatial omics assay.

graph_neighborhood(): Graph depth method based method to select niche

graph_path_length(): get path length in a graph

hclust_scores(): Hiearchal clustering of mapping scores for co mapping events

identify_markers(): identify_markers computes differential observation expression between selected territories.

image_plot(): image_plot - plotting vesalius embeddings

initialize_matches(): initialize matched data frame

int_sctransform(): SCTransform

integrate_assays(): integrate 2 vesalius assays

integrate_counts(): Integrate counts using Seurat

interlace_embeds(): interlace image stack between seed and query

internal_smooth(): internal smoothing function Function that does the smoothing on individual image array

isolate_territories(): isolating territories from vesalius image segments

vesalius: Spatial coordinates - alt

vesalius: Count matrix for vesalius - alt

joint_territories(): Jointly measured spatial omic assays territories

kmeans_segmentation(): kmeans segmentation function

knn_neighborhood(): k nearest neighbors - niche selection

layer_territory(): layer_territory generates layer from the outside to the inside of a territory

leiden_scores(): Using Leiden community clustering to for co-mapping events

leiden_segmentation(): leiden segmentation

log_norm(): log norm

louvain_scores(): Using Louvain community clustering to for co-mapping events

louvain_segmentation(): louvain segmentation

map_assays(): Aling and integrate spatial assay from the same modality using super pixels

map_index(): LAPVJ solver

match_cells(): Internal function returning cell type label match as numiric

merge_coordinates(): Merge coordinates from 2 vesalius assays

merge_territories(): Merge territories using specified labels

message_switch(): switch message output based in input

min_max(): min max normalisation

neighborhood_signal(): compute average expression of local neighborhood

niche_composition(): Method dispatch function for neighborhood selection - added flavor specific to composition

no_norm(): no norm

norm_pixel(): pixel normalisation dispatch function

optimize_matching(): optimize matching scores through batching

overlap_distance_matrix(): create a distance matrix based on mapping scores overlaps

pearson_approx(): compute fast pearson correlation between matrices

point_mapping(): mapping points between data sets

populate_graph(): populate graph with network connections

process_counts(): process counts

radius_neighborhood(): Radius based method to select niche

rasterise(): rasterise tiles

rebalence_colors(): rebalence colors

reduce_tensor_resolution(): reduce tensor resoltuon

regularise(): Internal regularise function. performs total variance regularisation

regularise_image(): regularise image

rename_counts(): renaming counts to remain consistent with vesalius nomenclature

score_matches(): Extract score from best matches

search_log(): search through log for parameter values or names

segment_image(): segment image

select_initial_indices(): select inital indices

signal_similarity(): compute the similarity between seed and query signals

smooth_image(): Smooth Image

summarise_territories(): summarise territories

territory_morphing(): territory_morphing applies morphological operators to a set of territoriees

territory_neighborhood(): Territory selection for large scale niche

territory_plot(): territory_plot - plotting Vesalius territories

tfidf_norm(): tf idf normalisation

unpack_territory_path(): retrieve the points contained in the edge of each territory

update_matches(): Update best matched cell pairs with new mapping costs

update_vesalius_assay(): update vesalius assay object

vesalius_assay-class: The vesalius_assay class

vesalius_deg(): Internal differantial gene expression function.

vesalius_deg_chisq(): chisq test for DEG

vesalius_deg_deseq2(): DESeq negatove binomail for DEG

vesalius_deg_edger(): edgeR functions for DEG

vesalius_deg_fisher(): Fisher's excat test for DEG

vesalius_deg_logit(): Logistic Regression for DEG

vesalius_deg_ttest(): t.test for DEG

vesalius_deg_wilcox(): wilcox rank sum test for DEG

vesalius vesalius_package vesalius-package: vesalius

view_gene_expression(): view_gene_expression