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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,29 +1,113 @@ | ||
| gpt_annot_check_plot <- function(checks, | ||
| items = c("annot_consist", | ||
| "checkable_count", | ||
| #"checkable_rate", | ||
| "true_pos_rate")){ | ||
| items = c("consistency_count","consistency_rate", | ||
| "consistency_stringent_count","consistency_stringent_rate", | ||
| # "checkable_count","checkable_rate", | ||
| "true_pos_count","true_pos_rate"), | ||
| metric_types=c("Rate","Count")[1], | ||
| scales = "free"){ | ||
| requireNamespace("ggplot2") | ||
|
|
||
| annotation <- value <- metric <- NULL; | ||
| annotation <- metric <- metric_category <- metric_type <- NULL; | ||
| check_df <- lapply(checks[items], | ||
| data.table::as.data.table, keep.rownames = TRUE) |> | ||
| data.table::rbindlist(idcol = "metric") |> | ||
| data.table::setnames(c("metric","annotation","value")) | ||
| check_df$metric <- factor(check_df$metric, levels = items, ordered = TRUE) | ||
|
|
||
| ggplot2::ggplot(check_df[annotation!="pheno_count"], | ||
| ggplot2::aes(x=annotation, y=value, fill=metric)) + | ||
| ggplot2::geom_bar(stat="identity") + | ||
| ggplot2::facet_grid(rows="metric", | ||
| scales = "free_y",) + | ||
| check_df$metric <- factor(check_df$metric, | ||
| levels = items, | ||
| ordered = TRUE) | ||
| check_df$annotation <- factor(check_df$annotation, | ||
| levels = unique(check_df$annotation), | ||
| ordered = TRUE) | ||
| # check_df[,row_count:=.N[!is.na(value)], by=c("metric","annotation")] | ||
| check_df[,metric_type:=ifelse(grepl("count",metric), | ||
| "Count",ifelse(grepl("rate",metric),"Rate",NA))] | ||
| check_df[,metric_category:=gsub("_count|_rate","",metric)] | ||
| check_df$metric_type <- factor(check_df$metric_type, ordered = TRUE) | ||
| check_df <- check_df[annotation!="pheno_count"] | ||
| combos <- expand.grid( | ||
| metric_category=check_df$metric_category, | ||
| metric_type=check_df$metric_type, | ||
| annotation=check_df$annotation | ||
| ) |> unique() |> `rownames<-`(NULL) | ||
| check_df2 <- merge(check_df, | ||
| combos, | ||
| by=c("metric_category","metric_type","annotation"), | ||
| all.y=TRUE) | ||
| # check_df[,label:=paste0("n=",value[metric_type=="Count"]), | ||
| # by=c("metric_category","annotation")] | ||
| check_df[,n:=value[metric_type=="Count"], | ||
| by=c("metric_category","annotation")] | ||
|
|
||
| plt <- ggplot2::ggplot(check_df[metric_type %in% metric_types], | ||
| ggplot2::aes(x=annotation, y=value, | ||
| fill=n, | ||
| label=round(value,2))) + | ||
| ggplot2::geom_bar(stat="identity", show.legend = TRUE) + | ||
| # ggplot2::scale_fill_viridis_d(drop = FALSE, end = .8 )+ | ||
| ggplot2::scale_fill_viridis_c()+ | ||
| ggplot2::scale_x_discrete(drop = scales %in% c("free","free_x")) + | ||
| ggplot2::facet_grid(facets=metric_type~metric_category, | ||
| scales = scales) + | ||
| ggplot2::theme_bw() + | ||
| ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 45, hjust = 1), | ||
| strip.background = ggplot2::element_rect(fill = "grey20"), | ||
| strip.text = ggplot2::element_text(color = "white")) + | ||
| ggplot2::labs(title = "GPT annotation validation", | ||
| x = "Annotation column", | ||
| y = "Value", | ||
| fill = "Metric") | ||
| strip.background = ggplot2::element_rect(fill = "grey20"), | ||
| strip.text = ggplot2::element_text(color = "white")) + | ||
| ggplot2::labs(x = "Annotation", | ||
| y = "Value", | ||
| fill = "N phenotypes") + | ||
| ggplot2::geom_label(fill='white') | ||
| # ggplot2::geom_text(angle=90, size=3, hjust=1.2) | ||
| # plt | ||
|
|
||
| if(scales %in% c("free","free_x")){ | ||
| plt <- plt+ | ||
| ggplot2::geom_vline(data = check_df2[is.na(value)], | ||
| ggplot2::aes(xintercept=annotation), | ||
| # label="N/A", | ||
| color="red", linetype="solid", linewidth=3, alpha=0.25) + | ||
| ggplot2::geom_text(data = check_df2[is.na(value)][,label:="N/A"], | ||
| ggplot2::aes(x=annotation, label=label, y=2), | ||
| position=ggplot2::position_fill(vjust = 0.1), | ||
| color="red", alpha=0.5, angle=90) | ||
| } | ||
| # count_df <- check_df[metric_type=="Count",,drop=FALSE] | ||
| # rate_df <- check_df[metric_type=="Rate",,drop=FALSE][annotation!="pheno_count"] | ||
| # plts <- list() | ||
| # make_plot <- function(df, | ||
| # y_lab=NULL){ | ||
| # p <- ggplot2::ggplot(df, | ||
| # ggplot2::aes(x=annotation, y=value, | ||
| # fill=metric_type)) + | ||
| # ggplot2::geom_bar(stat="identity", show.legend = FALSE) + | ||
| # ggplot2::scale_fill_viridis_d(drop=FALSE, end = .8 )+ | ||
| # ggplot2::scale_x_discrete(drop = FALSE) + | ||
| # ggplot2::facet_grid(rows="metric") + | ||
| # ggplot2::theme_bw() + | ||
| # ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 45, hjust = 1), | ||
| # strip.background = ggplot2::element_rect(fill = "grey20"), | ||
| # strip.text = ggplot2::element_text(color = "white")) + | ||
| # ggplot2::labs(x = "Annotation", | ||
| # y = y_lab, | ||
| # fill = "Metric") | ||
| # } | ||
| # if(nrow(count_df)>0){ | ||
| # plts[["count"]] <- make_plot(count_df,y_lab = "Count") | ||
| # } | ||
| # if(nrow(rate_df)>0){ | ||
| # plts[["rate"]] <- make_plot(rate_df,y_lab = "Rate") | ||
| # } | ||
| # if(length(plts)>1){ | ||
| # plts[[1]] <- plts[[1]] + | ||
| # ggplot2::theme(axis.text.x = ggplot2::element_blank()) | ||
| # } | ||
| # | ||
| # plt <- patchwork::wrap_plots(plts, ncol = 1, | ||
| # guides = "collect") + | ||
| # patchwork::plot_layout(axis_titles = "collect", | ||
| # axes = "collect") | ||
| return(list( | ||
| data=check_df, | ||
| plot=plt | ||
| )) | ||
| } |
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