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Added print method for amp_ordinate figure captions. Moved all print …
…methods to print_methods.R
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -37,6 +37,7 @@ Imports: | |
| cowplot, | ||
| readxl, | ||
| crayon, | ||
| cli, | ||
| biomformat, | ||
| doParallel, | ||
| foreach | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,79 @@ | ||
| #' Prints heatmap+functions plot (internal function) | ||
| #' | ||
| #' @param hmfunplot plot | ||
| #' | ||
| #' @export | ||
| #' @importFrom cowplot plot_grid | ||
| print.hmfunplot <- function(hmfunplot) { | ||
| print(cowplot::plot_grid(hmfunplot$heatmap, | ||
| hmfunplot$functions, | ||
| ncol = 2, | ||
| rel_widths = attributes(hmfunplot)[["rel_widths"]], | ||
| align = "h", | ||
| axis = "tb" | ||
| )) | ||
| } | ||
|
|
||
| #' Prints ampvis2 object summary (internal function) | ||
| #' | ||
| #' @param data (\emph{required}) Data list as loaded with \code{\link{amp_load}}. | ||
| #' | ||
| #' @importFrom crayon underline | ||
| #' @export | ||
| #' @author Kasper Skytte Andersen \email{kasperskytteandersen@@gmail.com} | ||
| print.ampvis2 <- function(data) { | ||
| ### calculate basic statistics and useful information about the data, print it | ||
| if (!isTRUE(attributes(data)$normalised)) { | ||
| # calculate basic stats and store in attributes for use in print.ampvis2 | ||
| readstats <- attributes(data)$readstats <- list( | ||
| "Total#Reads" = as.character(sum(data$abund)), | ||
| "Min#Reads" = as.character(min(colSums(data$abund))), | ||
| "Max#Reads" = as.character(max(colSums(data$abund))), | ||
| "Median#Reads" = as.character(median(colSums(data$abund))), | ||
| "Avg#Reads" = as.character(round(mean(colSums(data$abund)), digits = 2)) | ||
| ) | ||
| } else if (isTRUE(attributes(data)$normalised)) { | ||
| readstats <- attributes(data)$readstats | ||
| } | ||
| cat(class(data), "object with", length(data), "elements.", crayon::underline("\nSummary of OTU table:\n")) | ||
| print.table(c( | ||
| "Samples" = as.character(ncol(data$abund)), | ||
| "OTUs" = as.character(nrow(data$abund)), | ||
| readstats | ||
| ), | ||
| justify = "right" | ||
| ) | ||
| if (isTRUE(attributes(data)$normalised)) { | ||
| cat("(The read counts have been normalised)\n") | ||
| } | ||
| cat(crayon::underline("\nAssigned taxonomy:\n")) | ||
| print.table(c( | ||
| "Kingdom" = paste0(sum(nchar(data$tax$Kingdom) > 3), "(", round(sum(nchar(data$tax$Kingdom) > 3) / nrow(data$abund), digits = 2) * 100, "%)"), | ||
| "Phylum" = paste0(sum(nchar(data$tax$Phylum) > 3), "(", round(sum(nchar(data$tax$Phylum) > 3) / nrow(data$abund) * 100, digits = 2), "%)"), | ||
| "Class" = paste0(sum(nchar(data$tax$Class) > 3), "(", round(sum(nchar(data$tax$Class) > 3) / nrow(data$abund) * 100, digits = 2), "%)"), | ||
| "Order" = paste0(sum(nchar(data$tax$Order) > 3), "(", round(sum(nchar(data$tax$Order) > 3) / nrow(data$abund) * 100, digits = 2), "%)"), | ||
| "Family" = paste0(sum(nchar(data$tax$Family) > 3), "(", round(sum(nchar(data$tax$Family) > 3) / nrow(data$abund) * 100, digits = 2), "%)"), | ||
| "Genus" = paste0(sum(nchar(data$tax$Genus) > 3), "(", round(sum(nchar(data$tax$Genus) > 3) / nrow(data$abund) * 100, digits = 2), "%)"), | ||
| "Species" = paste0(sum(nchar(data$tax$Species) > 3), "(", round(sum(nchar(data$tax$Species) > 3) / nrow(data$abund) * 100, digits = 2), "%)") | ||
| ), | ||
| justify = "right" | ||
| ) | ||
| cat(crayon::underline("\nMetadata variables:"), as.character(ncol(data$metadata)), "\n", paste(as.character(colnames(data$metadata)), collapse = ", ")) | ||
| } | ||
|
|
||
| #' Print method for figure caption created by amp_ordinate | ||
| #' | ||
| #' @param captionwithrefs Character vector with the caption | ||
| #' | ||
| #' @importFrom cli cat_line rule | ||
| #' @importFrom crayon italic | ||
| #' @export | ||
| #' @author Kasper Skytte Andersen \email{kasperskytteandersen@@gmail.com} | ||
| print.figcaption <- function(captionwithrefs) { | ||
| cli::cat_line(cli::rule("Auto-generated figure caption (start)")) | ||
| captionwithrefs %>% | ||
| strwrap() %>% | ||
| crayon::italic() %>% | ||
| cli::cat_line() | ||
| cli::cat_line(cli::rule("Auto-generated figure caption (end)")) | ||
| } |
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