library(dplyr) library(ggplot2)
aberr_module <- params$aberr_module parsed_title <- dplyr::case_when( aberr_module == "dicentrics" ~ "Dicentrics curve fitting report", aberr_module == "translocations" ~ "Translocation FISH curve fitting report", aberr_module == "micronuclei" ~ "Micronuclei curve fitting report" )
r parsed_title
render_table <- function(x, font_size = NULL, ...) { knitr::kable(x, format = "latex", booktabs = TRUE, ...) %>% kableExtra::kable_styling( position = "center", latex_options = "HOLD_position", font_size = font_size ) }
# General parameters count_data <- params$fit_results_list[["fit_raw_data"]] fit_model_statistics <- params$fit_results_list[["fit_model_statistics"]] fit_model_summary <- params$fit_results_list[["fit_model_summary"]] fit_coeffs <- params$fit_results_list[["fit_coeffs"]] fit_var_cov_mat <- params$fit_results_list[["fit_var_cov_mat"]] fit_cor_mat <- params$fit_results_list[["fit_cor_mat"]] fit_formula_tex <- params$fit_results_list[["fit_formula_tex"]] gg_curve <- params$fit_results_list[["gg_curve"]] irr_conds <- params$fit_results_list[["irr_conds"]] # detection_lims <- params$fit_results_list[["detection_lims"]] # Translocations genome_factor <- params$fit_results_list[["genome_factor"]] chromosome_table <- params$fit_results_list[["chromosome_table"]] trans_sex <- params$fit_results_list[["trans_sex"]] frequency_select <- params$fit_results_list[["frequency_select"]]
r if (aberr_module == "translocations") {"# Chromosome data"}
r if (aberr_module == "translocations") {
paste("The analysed blood sample comes from a", trans_sex, "individual.")
}
if (aberr_module == "translocations") { num_cols <- as.numeric(ncol(chromosome_table)) chromosome_table %>% dplyr::mutate( dplyr::across( .cols = dplyr::everything(), .fns = function(x) { x <- ifelse(is.na(x) | x == "FALSE", "", x) x <- ifelse(x == "TRUE", "$\\checkmark$", x) return(x) } ) ) %>% render_table(align = "c", escape = FALSE) }
r if (aberr_module == "translocations") {
if (num_cols == 1) {
"where each chromosome was stained using M-FISH."
}
}
data <- count_data %>% biodosetools:::fix_count_data_names(type = "count", output = "kable") data$`$u$` <- kableExtra::cell_spec( x = data$`$u$`, background = ifelse(data$`$u$` > 1.96, "#ffc0cb", "white") ) data %>% render_table(align = "c", escape = FALSE)
r paste0("$$", fit_formula_tex, "$$")
r gsub("<=", "$\\\\leq$", fit_model_summary)
r if (aberr_module == "translocations") {"## Translocation frequency"}
r if (aberr_module == "translocations") {
paste("The fitting was performed using the ")
}
r if (aberr_module == "translocations") {
if (frequency_select == "full_gen_freq") {
paste("full genome translocation frequency.")
} else if (frequency_select == "measured_freq") {
paste("translocation frequency measured by FISH.")
}
}
r if (aberr_module == "translocations") {"## Genomic conversion factor"}
r if (aberr_module == "translocations") {
paste0("The genomic conversion factor to full genome is ", as.character(round(genome_factor, 3)), ".")
}
fit_coeffs %>% formatC(format = "e", digits = 3) %>% biodosetools:::fix_coeff_names(type = "rows", output = "kable") %>% render_table(align = "c", escape = FALSE)
fit_model_statistics %>% formatC(format = "f", digits = 3) %>% as.data.frame() %>% dplyr::mutate(df = as.integer(df)) %>% render_table(align = "c")
fit_cor_mat %>% biodosetools:::fix_coeff_names(type = "rows", output = "kable") %>% biodosetools:::fix_coeff_names(type = "cols", output = "kable") %>% formatC(format = "f", digits = 3) %>% render_table(align = "c", escape = FALSE)
fit_var_cov_mat %>% biodosetools:::fix_coeff_names(type = "rows", output = "kable") %>% biodosetools:::fix_coeff_names(type = "cols", output = "kable") %>% formatC(format = "e", digits = 3) %>% render_table(align = "c", escape = FALSE)
data.frame( matrix( unlist(irr_conds), nrow = length(irr_conds), byrow = TRUE ) ) %>% `colnames<-`(c("Characteristic", "Details")) %>% dplyr::mutate( Details = ifelse(Details == "", "Not specified", Details) ) %>% render_table(align = "l", linesep = "\\midrule") %>% kableExtra::column_spec(1, width = "4.5cm") %>% kableExtra::column_spec(2, width = "10cm")
gg_curve
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.