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# ----------------------------------------------------------------------------------------------------------------
#' Distribution of clonal status of single-cell TCR clonotypes
#'
#' @param contigList The product of TCR.ContigList() or BCR.ContigList().
#' @param sampleName The sample name of single cell sample.
#'
#' @return Multiple pictures in the form of a list.
#' @export
#' @import tidyr
#' @import dplyr
#' @import tibble
#' @import RColorBrewer
#' @import scales
#' @import ggplot2
#' @examples
#'
#' project_data_dir <- "F:/R_Language/data/tcr"
#' sample_name <- list.dirs(project_data_dir, full.names = FALSE, recursive = FALSE)
#' group_name <- c("A", "A", "B", "B")
#'
#' contig_list <- TCR.ContigList(project_data_dir, sample_name, group_name)
#'
#' TCR.ClonalStateDistribution(contig_list, sample_name)
#'
#' BasicPlot(TCR.ClonalStateDistribution, contig_list, sample_name)
#'
TCR.ClonalStateDistribution <- function(contigList, sampleName) {
CreateList <- function(contig_df, sampleNames) {
# --------------------
# clonotype distribution
clones_data <- contig_df %>%
dplyr::select(barcode, clonotype) %>%
unique() %>%
dplyr::add_count(clonotype) %>%
dplyr::rename(clonalState = n) %>%
dplyr::distinct(clonotype, clonalState, .keep_all = TRUE) %>%
dplyr::add_count(clonalState) %>%
dplyr::rename(frequency = n) %>%
dplyr::arrange(-frequency) %>%
dplyr::distinct(clonalState, frequency, .keep_all = TRUE) %>%
dplyr::arrange(clonalState) %>%
dplyr::mutate(clonalState = factor(clonalState))
friendly_cols <- c("#88CCEE", "#CC6677", "#DDCC77", "#117733", "#332288", "#AA4499", "#44AA99", "#999933", "#882255", "#661100", "#6699CC")
my_color_palette <- colorRampPalette(friendly_cols)(max(as.numeric(clones_data$clonalState)))
clones_data %>%
ggplot(aes(x = clonalState, y = frequency, fill = clonalState)) +
geom_bar(stat = "identity") + # my_theme
geom_text(aes(label = frequency), size = 4, vjust = 0, hjust = 0) +
coord_flip() +
scale_x_discrete(limits = rev) +
labs(title = sampleNames, x = "clonalState", y = "Barcode Frequency") +
scale_fill_manual(values = my_color_palette) +
theme_bw() +
theme(
legend.position = "none",
panel.border = element_blank(),
axis.line = element_line(),
text = element_text(size = 12),
strip.background = element_blank(),
plot.title = element_text(hjust = 0.5) # New
)
}
clones_plots <- purrr::pmap(list(contigList, sampleName), CreateList)
return(clones_plots)
}
# ----------------------------------------------------------------------------------------------------------------
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