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Merge pull request #154 from MoTrPAC/develop
v0.6.9: metab density plots
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| # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| #' @title QC Plot of proteomics reporter ion intensity data | ||
| #' | ||
| #' @description check whether results file is following guidelines | ||
| #' @param all_samples (vector) all sample ids | ||
| #' @param all_vial_labels (vector) only vial_labels | ||
| #' @param peprii (char) Reporter Ion Intensity df | ||
| #' @param isPTM (logical) Is a PTM assay | ||
| #' @param v_m (df) sample metadata | ||
| #' @param out_qc_folder (char) if `f_proof is TRUE`, a folder path can be provided | ||
| #' (otherwise print in current working directory) | ||
| #' @param output_prefix (char) provide a prefix for the output name | ||
| #' @param printPDF (logical) if `TRUE` (default print plots to pdf) | ||
| #' @param verbose (logical) `TRUE` (default) shows messages | ||
| #' @return (int) number of issues identified | ||
| #' @examples { | ||
| #' check_results(r_m = results_named, m_s = metadata_sample_named, m_m = metadata_metabolites_named) | ||
| #' } | ||
| #' @export | ||
| proteomics_plots_rii <- function(all_vial_labels, | ||
| all_samples, | ||
| peprii, | ||
| isPTM, | ||
| v_m, | ||
| out_qc_folder = NULL, | ||
| output_prefix, | ||
| printPDF, | ||
| verbose){ | ||
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| if(verbose) message(" + (+) PLOTS RII------------------") | ||
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| if( !is.null(all_vial_labels) ){ | ||
| required_columns <- get_required_columns(isPTM = isPTM, | ||
| prot_file = "rii") | ||
| required_columns <- c(required_columns, all_samples) | ||
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| if( all(required_columns %in% colnames(peprii)) ){ | ||
| # Check distributions | ||
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| if(isPTM){ | ||
| r_c <- c("ptm_peptide", all_samples) | ||
| fpeprii <- subset(peprii, select = r_c) | ||
| peptides_long <- fpeprii %>% tidyr::pivot_longer(cols = -c(ptm_peptide), | ||
| names_to = "vial_label", | ||
| values_to = "ri_intensity") | ||
| }else{ | ||
| r_c <- c("protein_id", "sequence", all_samples) | ||
| fpeprii <- subset(peprii, select = r_c) | ||
| peptides_long <- fpeprii %>% tidyr::pivot_longer(cols = -c(protein_id, sequence), | ||
| names_to = "vial_label", | ||
| values_to = "ri_intensity") | ||
| } | ||
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| # Plot Intensity distribution----- | ||
| if(verbose) message(" - (p) Plot intensity distributions") | ||
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| peptides_long <- merge(v_m, peptides_long, by = c("vial_label")) | ||
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| peptides_long$vial_label <- as.character(peptides_long$vial_label) | ||
| peptides_long$vial_label <- as.factor(peptides_long$vial_label) | ||
| peptides_long$tmt_plex <- as.factor(peptides_long$tmt_plex) | ||
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| pise <- ggplot2::ggplot(peptides_long, | ||
| aes(x = reorder(vial_label, log2(ri_intensity), FUN = median, na.rm = TRUE), | ||
| y = log2(ri_intensity), | ||
| fill = tmt_plex)) + | ||
| geom_boxplot(na.rm = TRUE) + | ||
| theme_linedraw() + | ||
| theme(axis.text.x = element_text(angle = 90, | ||
| hjust = 1, | ||
| vjust = 0.5, | ||
| size = 8)) + #legend.position = "none" | ||
| labs(x = "vial_label", y = "log2(ri_intensity)") + | ||
| labs(title = "Reporter Ion Intensity", | ||
| subtitle = output_prefix) | ||
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| # Plot NA values------ | ||
| if(verbose) message(" - (p) Plot NA values") | ||
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| p_na_peprii <- peprii[required_columns] %>% | ||
| inspectdf::inspect_na() %>% | ||
| dplyr::arrange(match(col_name, colnames(peprii))) %>% | ||
| inspectdf::show_plot() + | ||
| ylim(0, 100) + theme_linedraw() + | ||
| theme(axis.text.x = element_text(angle = 90, | ||
| hjust = 1, | ||
| vjust = 0.5, | ||
| size = 8)) | ||
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| # Plot unique IDs----- | ||
| if(verbose) message(" - (p) Plot Unique IDs") | ||
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| if(isPTM){ | ||
| key_id <- "ptm_peptide" | ||
| }else{ | ||
| key_id <- "protein_id" | ||
| } | ||
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| uid <- peptides_long %>% | ||
| group_by(across(all_of(c(key_id, "vial_label", "tmt_plex")))) %>% | ||
| summarise(total_rii = ri_intensity, .groups = 'drop') | ||
| uid2 <- uid[which(!is.na(uid$total_rii)),] | ||
| uid3 <- unique(uid2[c(key_id, "vial_label", "tmt_plex")]) %>% | ||
| count(vial_label, tmt_plex) | ||
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| puid1 <- ggplot(uid3, aes(x = reorder(vial_label, n), y = n, fill = tmt_plex)) + | ||
| geom_bar(stat = "identity") + | ||
| theme_linedraw() + | ||
| theme( | ||
| axis.text.x = element_text( | ||
| angle = 90, | ||
| hjust = 1, | ||
| vjust = 0.5, | ||
| size = 8 | ||
| ), | ||
| legend.position = "none" | ||
| ) + | ||
| geom_text( | ||
| aes(label = n), | ||
| # vjust = -0.5, | ||
| hjust = 1, | ||
| size = 2.7, | ||
| angle = 90 | ||
| ) + | ||
| ggtitle("RII: Unique IDs in samples") + | ||
| facet_wrap(~ tmt_plex, scales = "free") + | ||
| xlab("Vial Labels") | ||
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| puid2 <- ggplot(uid3, aes(x = reorder(vial_label, n), y = n, fill = tmt_plex)) + | ||
| geom_bar(stat = "identity", | ||
| na.rm = TRUE) + | ||
| theme_linedraw() + | ||
| theme( | ||
| axis.text.x = element_text( | ||
| angle = 90, | ||
| hjust = 1, | ||
| vjust = 0.5, | ||
| size = 8 | ||
| ) | ||
| ) + | ||
| geom_text( | ||
| aes(label = n), | ||
| # vjust = -0.5, | ||
| hjust = 1, | ||
| size = 2.7, | ||
| angle = 90 | ||
| ) + | ||
| ggtitle("RII: Unique IDs in samples") + | ||
| xlab("Vial Labels") | ||
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| if(is.null(out_qc_folder)){ | ||
| out_plot_dist <- paste0(output_prefix,"-qc-rii-distribution.pdf") | ||
| }else{ | ||
| out_plot_dist <- file.path(normalizePath(out_qc_folder), paste0(output_prefix,"-qc-rii-distribution.pdf")) | ||
| } | ||
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| if(printPDF) pdf(out_plot_dist, width = 12, height = 8) | ||
| print(pise) | ||
| print(puid1) | ||
| print(puid2) | ||
| print(p_na_peprii) | ||
| if(printPDF) garbage <- dev.off() | ||
| }else{ | ||
| if(verbose) message(" - (-) Not all required columns available in RII: print proof is not possible") | ||
| required_columns[!(required_columns %in% colnames(peprii))] | ||
| ic <- ic + 1 | ||
| } | ||
| } # !is.null(all_vial_labels) | ||
| } |
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