Take a raw expression counts, cell type annotations, and positional cooridnates to identify CNA patterns across space and CNA-based clustering patterns
run_slide_cna(
counts,
beads_df,
gene_pos,
output_directory,
plot_directory,
spatial = TRUE,
roll_mean_window = 101,
avg_bead_per_bin = 12,
pos = TRUE,
pos_k = 55,
ex_k = 1,
hc_function_bin = "ward.D2",
spatial_vars_to_plot = c("seurat_clusters", "bin_all", "N_bin", "umi_bin",
"cluster_type"),
scale_bin_thresh_hard = TRUE,
lower_bound_cnv = 0.6,
upper_bound_cnv = 1.4,
hc_function_cnv = "ward.D2",
hc_function_cnv_heatmap = "ward.D2",
quantile_plot_cluster_label = "seurat_clusters",
hc_function_silhouette = "ward.D2",
max_k_silhouette = 10,
plot_silhouette = TRUE,
hc_function_plot_clones = "ward.D2",
use_GO_terms = TRUE,
chrom_ord = c("chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9",
"chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18",
"chr19", "chr20", "chr21", "chr22", "chr23", "chrX", "chrY", "chrM"),
chrom_colors = c(chr1 = "#8DD3C7", chr2 = "#FFFFB3", chr3 = "#BEBADA", chr4 =
"#FB8072", chr5 = "#80B1D3", chr6 = "#FDB462", chr7 = "#B3DE69", chr8 = "#FCCDE5",
chr9 = "#D9D9D9", chr10 = "#BC80BD", chr11 = "#CCEBC5", chr12 = "#FFED6F", chr13 =
"#1B9E77", chr14 = "#D95F02", chr15 = "#7570B3", chr16 = "#E7298A", chr17 =
"#66A61E", chr18 = "#E6AB02", chr19 = "#A6761D", chr20 = "#666666", chr21 =
"#A6CEE3", chr22 = "#1F78B4", chrX = "#B2DF8A"),
text_size = 16,
title_size = 18,
legend_size_pt = 4,
legend_height_bar = 1.5
)None
data.frame of raw counts (genes x beads)
data.frame of annotation of each bead (beads x annotations); contains columns 'bc' for bead names, 'cluster_type' for annotations of 'Normal' or 'Malignant', 'pos_x' for x-coordinate bead positions, and 'pos_y' for y-coordinate bead positions
data.frame with columns for GENE, chr, start, end, rel_gene_pos (1 : # of genes on chromosome)
output directory path
output plot directory path
TRUE if using spatial information FALSE if not
integer number of adjacent genes for which to average over in pyramidal weighting scheme
integer of average number of beads there should be per bin
TRUE if doing spatial and expressional binning, FALSE if just expressional binning
positional weight
expressional weight
hierarchical clustering function for binning; to feed hclust's method argument, one of "ward.D", "ward.D2", "single", "complete", "average", "mcquitty", "median" or "centroid"
character vector of features to plot/columns of metadata
TRUE if using strict thresholds for expression thresholds and FALSE if adjusting thresholds based on 1 + or - the mean of absolute min and max vlaues
numeric float to represent the lower cap for CNV scores
numeric float to represent the upper cap for CNV scores
character for which hierarchical clustering function to use for CNV-calling; to feed hclust's method argument, one of "ward.D", "ward.D2", "single", "complete", "average", "mcquitty", "median" or "centroid"
character for which hierarchical clustering function to use for visualzing CNV heat map; to feed hclust's method argument, one of "ward.D", "ward.D2", "single", "complete", "average", "mcquitty", "median" or "centroid"
character string of which column name to keep in quantile plot
character string for which hierarchical clustering function to use for the Silhouette method; to feed hclust's method argument, one of "ward.D", "ward.D2", "single", "complete", "average", "mcquitty", "median" or "centroid"
integer of number max number of clusters to evaluate (2:max_k_silhouette) . in Silhouette method
TRUE if plotting silhouette scores for clustering
character string for which hierarchical clustering function to use in plotting clones
TRUE if using enrichR to get Gene Ontology terms for SlideCNA-defined clusters
character vector of order and names of chromosomes
character vector of which colors each chromosome should be in heat map
integer of size of text in some ggplots
integer of size of title in some ggplots
integer of size of legend text size in some ggplots
integer of height of legend bar in some ggplots