From 9faa71dfadc4264bd98cc8c42c9ccddd8bf60147 Mon Sep 17 00:00:00 2001 From: nahid18 Date: Tue, 18 Jun 2024 16:54:15 +0600 Subject: [PATCH] feat: metadata and motif --- NAMESPACE | 2 +- R/get_study.R | 27 ++++--- R/retcr_proj_class.R | 20 ++++-- R/utils-motif-plot.R | 25 ++++--- R/utils-motif.R | 72 +++++++++---------- README.md | 44 +++++++++--- inst/extdata/PRJNA473147_metadata_file.csv | 76 ++++++++++++++++++++ man/Motif-class.Rd | 8 ++- man/get_study.Rd | 2 +- man/{plot_motif_counts.Rd => plot_motifs.Rd} | 12 ++-- man/reTCRProj-class.Rd | 6 +- 11 files changed, 211 insertions(+), 83 deletions(-) create mode 100644 inst/extdata/PRJNA473147_metadata_file.csv rename man/{plot_motif_counts.Rd => plot_motifs.Rd} (62%) diff --git a/NAMESPACE b/NAMESPACE index 04883e4..c02049a 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -8,7 +8,7 @@ export(plot_clonal_prop_per_group) export(plot_clonal_prop_per_sample) export(plot_clonotype_abundance) export(plot_diversity_index) -export(plot_motif_counts) +export(plot_motifs) export(plot_reads_group_abundance) exportClasses(Basic) exportClasses(Clonality) diff --git a/R/get_study.R b/R/get_study.R index 5a651f4..64df714 100644 --- a/R/get_study.R +++ b/R/get_study.R @@ -1,6 +1,7 @@ source("R/utils-diversity.R") source("R/utils-clonality.R") source("R/utils-basic.R") +source("R/utils-motif.R") source("R/utils-hill.R") #' Get pyTCR data of a project @@ -14,25 +15,33 @@ source("R/utils-hill.R") #' #' @examples #' \dontrun{ -#' proj <- reTCR::get_study(id = "PRJNA473147", attr_col = "cmv_status") +#' proj <- reTCR::get_study(id="PRJNA473147", attr_col="cmv_status") #' } get_study <- function(id, attr_col) { stopifnot(is.character(id) && nchar(id) > 0) - filename <- paste0(id, "_mixcr_metadata_file.csv") - filepath <- system.file("extdata", filename, package = "reTCR") - data <- utils::read.csv(filepath) - basic <- .get_basic(data = data, attr_col = attr_col) - diversity <- .get_diversity(data = data, attr_col = attr_col) - clonality <- .get_clonality(data = data, attr_col = attr_col) - hill <- .get_hill_numbers(df = data) + samplefile <- paste0(id, "_metadata_file.csv") + samplepath <- system.file("extdata", samplefile, package = "reTCR") + sampledata <- utils::read.csv(samplepath) + + mixfile <- paste0(id, "_mixcr_metadata_file.csv") + mixpath <- system.file("extdata", mixfile, package = "reTCR") + mixdata <- utils::read.csv(mixpath) + + basic <- .get_basic(data = mixdata, attr_col = attr_col) + diversity <- .get_diversity(data = mixdata, attr_col = attr_col) + clonality <- .get_clonality(data = mixdata, attr_col = attr_col) + motif <- .get_motif(data = mixdata, attr_col = attr_col) + hill <- .get_hill_numbers(df = mixdata) return(methods::new( "reTCRProj", - data = data, + data = mixdata, + metadata = sampledata, basic = basic, diversity = diversity, clonality = clonality, + motif = motif, hill = hill )) } diff --git a/R/retcr_proj_class.R b/R/retcr_proj_class.R index 026042e..30c7bcf 100644 --- a/R/retcr_proj_class.R +++ b/R/retcr_proj_class.R @@ -72,15 +72,17 @@ setClass("Clonality", #' #' A class to represent motif metrics #' -#' @slot aa_spectratype aa spectratype data -#' @slot aa_max_spectratype aa max spectratype data -#' @slot aa_motif_count aa motif count data +#' @slot aa_spectra Amino acid spectratype +#' @slot aa_max_spectra Amino acid max spectratype +#' @slot aa_motif_count Amino acid motif count table +#' @slot aa_most_motif Most abundant amino acid motif per sample #' @exportClass Motif setClass("Motif", slots = c( - aa_spectratype = "data.frame", - aa_max_spectratype = "data.frame", - aa_motif_count = "data.frame" + aa_spectra = "data.frame", + aa_max_spectra = "data.frame", + aa_motif_count = "data.frame", + aa_most_motif = "data.frame" ) ) @@ -88,18 +90,22 @@ setClass("Motif", #' #' A class to represent a reTCR project #' -#' @slot data contains the main data for the project +#' @slot data contains the MIXCR data for the project +#' @slot metadata contains the sample metadata #' @slot basic contains basic metrics #' @slot diversity contains diversity metrics #' @slot clonality contains clonality metrics +#' @slot motif contains motif metrics #' @slot hill contains Hill numbers #' @exportClass reTCRProj setClass("reTCRProj", slots = c( data = "data.frame", + metadata = "data.frame", basic = "Basic", diversity = "Diversity", clonality = "Clonality", + motif = "Motif", hill = "data.frame" ) ) diff --git a/R/utils-motif-plot.R b/R/utils-motif-plot.R index 773ff46..c528d2e 100644 --- a/R/utils-motif-plot.R +++ b/R/utils-motif-plot.R @@ -3,7 +3,8 @@ #' This function plots the motif counts. #' #' @param data A data frame containing the motif counts. -#' @param threshold the minimum count threshold (default: 60). +#' @param k the minimum count threshold (default: 60). +#' @param attr_col Character. Attribute column name. #' #' @return A ggplot2 object representing the motif counts plot. #' @export @@ -11,28 +12,32 @@ #' @examples #' \dontrun{ #' proj <- reTCR::get_study(id="PRJNA473147", attr_col="cmv_status") -#' reTCR::plot_motif_counts(proj@motif@aa_motif_count, 20) +#' reTCR::plot_motifs(proj@motif@aa_motif_count, "cmv_status", 50) #' } -plot_motif_counts <- function(data, threshold = 60) { - data <- dplyr::filter(data, count > threshold) - df <- stats::aggregate(count ~ cmv_status + motif, data = data, FUN = length) +plot_motifs <- function(data, attr_col, k = 60) { + data <- dplyr::filter(data, count > k) + df <- stats::aggregate( + count ~ cmv_status + motif, + data = data, + FUN = length + ) colnames(df)[3] <- "number_of_samples" df <- dplyr::filter(df, number_of_samples > 2) - data <- dplyr::inner_join(data, df, by = c("cmv_status", "motif")) + data <- dplyr::inner_join(data, df, by = c(attr_col, "motif")) ggplot2::ggplot( data, ggplot2::aes( x = motif, y = count, - color = cmv_status + color = attr_col ) ) + ggplot2::geom_jitter(width = 0.2, size = 3) + ggplot2::labs( - x = "Amino acid motif", - y = "Count", - color = "CMV Status" + x = "motif", + y = "count", + color = "status" ) + ggplot2::theme_bw() + ggplot2::theme( diff --git a/R/utils-motif.R b/R/utils-motif.R index f349483..93423a8 100644 --- a/R/utils-motif.R +++ b/R/utils-motif.R @@ -1,15 +1,4 @@ -.get_aa_spectratype <- function(data) { - aa_spec <- data %>% - dplyr::mutate(aa_length = nchar(cdr3aa)) %>% - dplyr::group_by(sample, cmv_status, aa_length) %>% - dplyr::summarise( - spectratype = sum(freq, na.rm = TRUE), - .groups = "drop" - ) - return(aa_spec) -} - -.get_most_freq_aa_spectratype <- function(aa_spec) { +.get_most_freq_aa_spec <- function(aa_spec) { aa_max <- aa_spec %>% dplyr::group_by(sample) %>% dplyr::slice_max(spectratype, n = 1) @@ -27,51 +16,60 @@ return(aa_motif_list) } -.get_aa_motif_count <- function(data, aa_max) { +.get_aa_motif_count <- function(data, aa_max, attr_col) { + return(aa_motif_count) +} + +.get_motif <- function(data, attr_col) { + aa_spec <- data %>% + dplyr::mutate(aa_length = nchar(cdr3aa)) %>% + dplyr::group_by(sample, !!rlang::sym(attr_col), aa_length) %>% + dplyr::summarise( + spectratype = sum(freq, na.rm = TRUE), + .groups = "drop" + ) + + aa_max <- aa_spec %>% + dplyr::group_by(sample) %>% + dplyr::slice_max(spectratype, n = 1) + + # aa motif count table samples <- unique(data$sample) - aa_motif <- dplyr::tibble( + aa_motif_tb <- dplyr::tibble( motif = character(), count = numeric(), sample = character() ) + for (sample in samples) { - data_temp <- data %>% dplyr::filter(.data$sample == !!sample) - motif_counts <- .get_aa_motif_list(data_temp$cdr3aa, 6) + data_temp <- data %>% dplyr::filter(data$sample == !!sample) + motif_list <- .get_aa_motif_list(data_temp$cdr3aa, 6) data_temp <- dplyr::tibble( - motif = names(motif_counts), - count = as.numeric(unlist(motif_counts)), + motif = names(motif_list), + count = as.numeric(unlist(motif_list)), sample = sample ) - aa_motif <- dplyr::bind_rows(aa_motif, data_temp) + aa_motif_tb <- dplyr::bind_rows(aa_motif_tb, data_temp) } + aa_motif_count <- dplyr::left_join( - aa_motif, - dplyr::select(aa_max, sample, cmv_status), + aa_motif_tb, + dplyr::select(aa_max, sample, !!rlang::sym(attr_col)), by = "sample" ) - return(aa_motif_count) -} -.get_most_motif_per_sample <- function(data) { - aa_max <- data %>% + # most abundant motif per sample + aa_most_abundant_motif <- aa_motif_count %>% dplyr::group_by(sample) %>% - dplyr::slice_max(freq, n = 1) - return(aa_max) -} - -.get_motif <- function(data) { - aa_spec <- .get_aa_spectratype(data) - aa_max <- .get_most_freq_aa_spectratype(aa_spec) - aa_motif_count <- .get_aa_motif_count(data, aa_max) - aa_most_abundant_motif <- .get_most_motif_per_sample(aa_motif_count) + dplyr::slice_max(count, n = 1) return( methods::new( "Motif", - aa_spectratype = aa_spec, - aa_max_spectratype = aa_max, + aa_spectra = aa_spec, + aa_max_spectra = aa_max, aa_motif_count = aa_motif_count, - aa_most_abundant_motif = aa_most_abundant_motif + aa_most_motif = aa_most_abundant_motif ) ) } diff --git a/README.md b/README.md index dd6480d..eb21b83 100644 --- a/README.md +++ b/README.md @@ -25,11 +25,14 @@ library(reTCR) proj <- reTCR::get_study(id="PRJNA473147", attr_col="cmv_status") -# view data +# get MIXCR data print(proj@data) + +# get sample metadata +print(proj@metadata) ``` -## 1. Basic Metrics +## 1. Basic metrics ```r # summary data @@ -57,7 +60,7 @@ print(proj@basic@convergence) print(proj@basic@spectratype) ``` -### 1.2 Statistical Analysis +### 1.2 Statistical analysis D'Agostino normality test @@ -77,7 +80,7 @@ library(stats) shapiro.test(proj@basic@summary_data$clonotype_count) ``` -## 2. Diversity Metrics +## 2. Diversity metrics ```r # shannon index values @@ -96,7 +99,7 @@ print(proj@diversity@chao1) print(proj@diversity@gini_coeff) ``` -### 2.2 Diversity Visualization +### 2.2 Diversity visualization ```r reTCR::plot_diversity_index(proj@diversity@shannon, "shannon_index", "cmv_status") @@ -114,7 +117,7 @@ reTCR::plot_diversity_index(proj@diversity@chao1, "chao1", "cmv_status") reTCR::plot_diversity_index(proj@diversity@gini_coeff, "gini_coeff", "cmv_status") ``` -## 3. Clonality Metrics +## 3. Clonality metrics ```r # most frequent clonotypes @@ -139,7 +142,7 @@ print(proj@clonality@abundance_top) print(proj@clonality@abundance_rare) ``` -### 3.2 Clonality Visualization +### 3.2 Clonality visualization ```r # let's store clonal proportion in `clonal_data` @@ -161,7 +164,30 @@ reTCR::plot_reads_group_abundance(proj@clonality@abundance_top) reTCR::plot_reads_group_abundance(proj@clonality@abundance_rare) ``` -## 4. Segment usage metrics +## 4. Motif metrics + +```r +# Amino acid spectratype +print(proj@motif@aa_spectra) + +# Amino acid max spectratype +print(proj@motif@aa_max_spectra) + +# Amino acid motif count table +print(proj@motif@aa_motif_count) + +# Most abundant amino acid motif per sample +print(proj@motif@aa_most_motif) +``` + +### 4.2 Motif visualization + +```r +# plot amino acid motif counts +reTCR::plot_motifs(proj@motif@aa_motif_count, "cmv_status", 20) +``` + +## 5. Segment usage metrics ```r # Top n highest clonotypes @@ -171,7 +197,7 @@ reTCR::get_top_n_clonotypes(proj@data, 15, "cmv_status") reTCR::get_bottom_n_clonotypes(proj@data, 20, "cmv_status") ``` -## 5. Hill numbers +## 6. Hill numbers ```r # get hill numbers diff --git a/inst/extdata/PRJNA473147_metadata_file.csv b/inst/extdata/PRJNA473147_metadata_file.csv new file mode 100644 index 0000000..e9483ba --- /dev/null +++ b/inst/extdata/PRJNA473147_metadata_file.csv @@ -0,0 +1,76 @@ +Sample,Assay Type,AvgSpotLen,Bases,BioProject,BioSample,Bytes,cell_subpopulation,Center Name,clonotype_count,cmv_peptide,cmv_status,Consent,DATASTORE filetype,DATASTORE provider,DATASTORE region,Experiment,GEO_Accession (exp),Instrument,LibraryLayout,LibrarySelection,LibrarySource,Organism,Platform,productive_reads,ReleaseDate,create_date,version,Sample Name,source_name,SRA Study +SRR8181389,OTHER,249,2943502790,PRJNA473147,SAMN10414187,1233479503,CD8-enriched,GEO,1086147,CRVLCCYVL,positive,public,"run.zq,fastq,sra","s3,ncbi,gs","gs.us-east1,s3.us-east-1,ncbi.public",SRX5001383,GSM3466797,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo 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HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,7438191,2018-11-23T00:00:00Z,2018-05-25T13:49:00Z,1,GSM3155094,peripheral blood mononuclear cells,SRP148992 +SRR7219381,OTHER,348,3046400641,PRJNA473147,SAMN09261067,1680300873,CD8-enriched,GEO,37234,TPRVTGGGAM,positive,public,"sra,run.zq,fastq","gs,ncbi,s3","gs.us-east1,ncbi.public,s3.us-east-1",SRX4125929,GSM3155095,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,8134892,2018-11-23T00:00:00Z,2018-05-25T13:44:00Z,1,GSM3155095,peripheral blood mononuclear cells,SRP148992 +SRR7219382,OTHER,299,1506316509,PRJNA473147,SAMN09261066,836267774,unsorted,GEO,403105,none,positive,public,"run.zq,sra,fastq","ncbi,gs,s3","ncbi.public,gs.us-east1,s3.us-east-1",SRX4125930,GSM3155096,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,4461887,2018-11-23T00:00:00Z,2018-05-25T13:44:00Z,1,GSM3155096,peripheral blood mononuclear cells,SRP148992 +SRR7219383,OTHER,299,1450146953,PRJNA473147,SAMN09261065,798804253,unsorted,GEO,779479,CRVLCCYVL,positive,public,"sra,fastq,run.zq","ncbi,s3,gs","s3.us-east-1,gs.us-east1,ncbi.public",SRX4125931,GSM3155097,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,4334321,2018-11-23T00:00:00Z,2018-05-25T13:42:00Z,1,GSM3155097,peripheral blood mononuclear cells,SRP148992 +SRR7219384,OTHER,299,969370883,PRJNA473147,SAMN09261064,540109312,unsorted,GEO,507295,FRCPRRFCF,positive,public,"run.zq,sra,fastq","gs,s3,ncbi","gs.us-east1,s3.us-east-1,ncbi.public",SRX4125932,GSM3155098,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,2893655,2018-11-23T00:00:00Z,2018-05-25T13:40:00Z,1,GSM3155098,peripheral blood mononuclear cells,SRP148992 +SRR7219385,OTHER,299,1578398101,PRJNA473147,SAMN09261063,871305731,unsorted,GEO,623779,TPRVTGGGAM,positive,public,"sra,fastq,run.zq","gs,ncbi,s3","ncbi.public,s3.us-east-1,gs.us-east1",SRX4125933,GSM3155099,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,4708088,2018-11-23T00:00:00Z,2018-05-25T13:41:00Z,1,GSM3155099,peripheral blood mononuclear cells,SRP148992 +SRR7219386,OTHER,299,1484217743,PRJNA473147,SAMN09261062,821420665,unsorted,GEO,584506,none,positive,public,"fastq,sra,run.zq","ncbi,gs,s3","s3.us-east-1,ncbi.public,gs.us-east1",SRX4125934,GSM3155100,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,4536124,2018-11-23T00:00:00Z,2018-05-25T13:42:00Z,1,GSM3155100,peripheral blood mononuclear cells,SRP148992 +SRR7219387,OTHER,299,1382780998,PRJNA473147,SAMN09261061,763777752,unsorted,GEO,538597,CRVLCCYVL,positive,public,"run.zq,fastq,sra","ncbi,gs,s3","s3.us-east-1,ncbi.public,gs.us-east1",SRX4125935,GSM3155101,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,4138428,2018-11-23T00:00:00Z,2018-05-25T13:41:00Z,1,GSM3155101,peripheral blood mononuclear cells,SRP148992 +SRR7219388,OTHER,299,1699129911,PRJNA473147,SAMN09261060,919337903,unsorted,GEO,305592,FRCPRRFCF,positive,public,"run.zq,fastq,sra","gs,s3,ncbi","gs.us-east1,s3.us-east-1,ncbi.public",SRX4125936,GSM3155102,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,5240440,2018-11-23T00:00:00Z,2018-05-25T13:42:00Z,1,GSM3155102,peripheral blood mononuclear cells,SRP148992 +SRR7219389,OTHER,299,1181219858,PRJNA473147,SAMN09261121,653704313,unsorted,GEO,386160,RPHERNGFTVL,positive,public,"run.zq,fastq,sra","ncbi,s3,gs","s3.us-east-1,ncbi.public,gs.us-east1",SRX4125937,GSM3155103,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,3547381,2018-11-23T00:00:00Z,2018-05-25T13:41:00Z,1,GSM3155103,peripheral blood mononuclear cells,SRP148992 +SRR7219390,OTHER,299,1530970362,PRJNA473147,SAMN09261120,852885314,unsorted,GEO,337660,TPRVTGGGAM,positive,public,"sra,fastq,run.zq","gs,s3,ncbi","gs.us-east1,s3.us-east-1,ncbi.public",SRX4125938,GSM3155104,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,4710517,2018-11-23T00:00:00Z,2018-05-25T13:44:00Z,1,GSM3155104,peripheral blood mononuclear cells,SRP148992 +SRR7219391,OTHER,135,395299440,PRJNA473147,SAMN09261119,245337134,CD8-enriched,GEO,212125,none,positive,public,"fastq,run.zq,sra","s3,gs,ncbi","s3.us-east-1,ncbi.public,gs.us-east1",SRX4125939,GSM3155105,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,963210,2018-11-23T00:00:00Z,2018-05-25T13:40:00Z,1,GSM3155105,peripheral blood mononuclear cells,SRP148992 +SRR7219392,OTHER,135,625922370,PRJNA473147,SAMN09261118,381989516,CD8-enriched,GEO,59739,CRVLCCYVL,positive,public,"run.zq,fastq,sra","ncbi,s3,gs","s3.us-east-1,ncbi.public,gs.us-east1",SRX4125940,GSM3155106,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,1592670,2018-11-23T00:00:00Z,2018-05-25T13:40:00Z,1,GSM3155106,peripheral blood mononuclear cells,SRP148992 +SRR7219393,OTHER,135,624576960,PRJNA473147,SAMN09261117,385123883,CD8-enriched,GEO,75470,FRCPRRFCF,positive,public,"sra,fastq,run.zq","gs,s3,ncbi","gs.us-east1,ncbi.public,s3.us-east-1",SRX4125941,GSM3155107,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,1440428,2018-11-23T00:00:00Z,2018-05-25T13:40:00Z,1,GSM3155107,peripheral blood mononuclear cells,SRP148992 +SRR7219394,OTHER,135,587313720,PRJNA473147,SAMN09261116,365479944,CD8-enriched,GEO,200167,RPHERNGFTVL,positive,public,"run.zq,sra,fastq","s3,ncbi,gs","ncbi.public,s3.us-east-1,gs.us-east1",SRX4125942,GSM3155108,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,1375678,2018-11-23T00:00:00Z,2018-05-25T13:40:00Z,1,GSM3155108,peripheral blood mononuclear cells,SRP148992 +SRR7219395,OTHER,135,541809540,PRJNA473147,SAMN09261115,332984206,CD8-enriched,GEO,84142,TPRVTGGGAM,positive,public,"fastq,sra,run.zq","s3,ncbi,gs","gs.us-east1,s3.us-east-1,ncbi.public",SRX4125943,GSM3155109,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,1425865,2018-11-23T00:00:00Z,2018-05-25T13:41:00Z,1,GSM3155109,peripheral blood mononuclear cells,SRP148992 +SRR7219396,OTHER,249,3506144684,PRJNA473147,SAMN09261114,1429171567,CD8-enriched,GEO,283478,none,positive,public,"run.zq,fastq,sra","gs,s3,ncbi","gs.us-east1,ncbi.public,s3.us-east-1",SRX4125944,GSM3155110,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,13028045,2018-11-23T00:00:00Z,2018-05-25T13:48:00Z,1,GSM3155110,peripheral blood mononuclear cells,SRP148992 +SRR7219397,OTHER,249,3858334540,PRJNA473147,SAMN09261113,1497871800,CD8-enriched,GEO,81340,CRVLCCYVL,positive,public,"fastq,run.zq,sra","gs,ncbi,s3","ncbi.public,gs.us-east1,s3.us-east-1",SRX4125945,GSM3155111,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,15000704,2018-11-23T00:00:00Z,2018-05-25T13:45:00Z,1,GSM3155111,peripheral blood mononuclear cells,SRP148992 +SRR7219398,OTHER,249,6592866588,PRJNA473147,SAMN09261112,2620745311,CD8-enriched,GEO,25723,FRCPRRFCF,positive,public,"sra,run.zq,fastq","gs,ncbi,s3","ncbi.public,s3.us-east-1,gs.us-east1",SRX4125946,GSM3155112,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,25588668,2018-11-23T00:00:00Z,2018-05-25T13:51:00Z,1,GSM3155112,peripheral blood mononuclear cells,SRP148992 +SRR7219399,OTHER,249,4272139725,PRJNA473147,SAMN09261111,1747452329,CD8-enriched,GEO,132349,RPHERNGFTVL,positive,public,"sra,fastq,run.zq","s3,ncbi,gs","gs.us-east1,s3.us-east-1,ncbi.public",SRX4125947,GSM3155113,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,16294617,2018-11-23T00:00:00Z,2018-05-25T13:46:00Z,1,GSM3155113,peripheral blood mononuclear cells,SRP148992 +SRR7219400,OTHER,249,3441680841,PRJNA473147,SAMN09261110,1390918799,CD8-enriched,GEO,122888,TPRVTGGGAM,positive,public,"fastq,run.zq,sra","s3,gs,ncbi","s3.us-east-1,ncbi.public,gs.us-east1",SRX4125948,GSM3155114,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,13010720,2018-11-23T00:00:00Z,2018-05-25T13:45:00Z,1,GSM3155114,peripheral blood mononuclear cells,SRP148992 +SRR7219401,OTHER,135,395647470,PRJNA473147,SAMN09261109,247443509,CD8-enriched,GEO,183707,none,positive,public,"fastq,sra,run.zq","gs,s3,ncbi","s3.us-east-1,ncbi.public,gs.us-east1",SRX4125949,GSM3155115,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,1042812,2018-11-23T00:00:00Z,2018-05-25T13:39:00Z,1,GSM3155115,peripheral blood mononuclear cells,SRP148992 +SRR7219402,OTHER,135,901135530,PRJNA473147,SAMN09261108,527955904,CD8-enriched,GEO,55471,CRVLCCYVL,positive,public,"sra,fastq,run.zq","s3,ncbi,gs","ncbi.public,s3.us-east-1,gs.us-east1",SRX4125950,GSM3155116,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,2425994,2018-11-23T00:00:00Z,2018-05-25T13:41:00Z,1,GSM3155116,peripheral blood mononuclear cells,SRP148992 +SRR7219403,OTHER,135,711659790,PRJNA473147,SAMN09261041,435141576,CD8-enriched,GEO,31431,FRCPRRFCF,positive,public,"fastq,sra,run.zq","ncbi,gs,s3","ncbi.public,gs.us-east1,s3.us-east-1",SRX4125951,GSM3155117,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,1899999,2018-11-23T00:00:00Z,2018-05-25T13:41:00Z,1,GSM3155117,peripheral blood mononuclear cells,SRP148992 +SRR7219404,OTHER,135,384522930,PRJNA473147,SAMN09261040,238934877,CD8-enriched,GEO,60619,RPHERNGFTVL,positive,public,"run.zq,sra,fastq","gs,ncbi,s3","s3.us-east-1,ncbi.public,gs.us-east1",SRX4125952,GSM3155118,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,938285,2018-11-23T00:00:00Z,2018-05-25T13:39:00Z,1,GSM3155118,peripheral blood mononuclear cells,SRP148992 +SRR7219405,OTHER,135,688849380,PRJNA473147,SAMN09261102,421548272,CD8-enriched,GEO,64580,TPRVTGGGAM,positive,public,"run.zq,fastq,sra","s3,ncbi,gs","ncbi.public,s3.us-east-1,gs.us-east1",SRX4125953,GSM3155119,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,1802570,2018-11-23T00:00:00Z,2018-05-25T13:40:00Z,1,GSM3155119,peripheral blood mononuclear cells,SRP148992 +SRR7219406,OTHER,249,1335245038,PRJNA473147,SAMN09261107,569530361,CD8-enriched,GEO,256394,none,positive,public,"run.zq,sra,fastq","ncbi,s3,gs","ncbi.public,s3.us-east-1,gs.us-east1",SRX4125954,GSM3155120,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,4821591,2018-11-23T00:00:00Z,2018-05-25T13:47:00Z,1,GSM3155120,peripheral blood mononuclear cells,SRP148992 +SRR7219407,OTHER,249,2344133845,PRJNA473147,SAMN09261074,980342920,CD8-enriched,GEO,121384,CRVLCCYVL,positive,public,"sra,run.zq,fastq","ncbi,gs,s3","s3.us-east-1,gs.us-east1,ncbi.public",SRX4125955,GSM3155121,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,8951471,2018-11-23T00:00:00Z,2018-05-25T13:43:00Z,1,GSM3155121,peripheral blood mononuclear cells,SRP148992 +SRR7219408,OTHER,249,1951515984,PRJNA473147,SAMN09261073,817961426,CD8-enriched,GEO,97686,FRCPRRFCF,positive,public,"run.zq,sra,fastq","ncbi,s3,gs","s3.us-east-1,gs.us-east1,ncbi.public",SRX4125956,GSM3155122,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,7263340,2018-11-23T00:00:00Z,2018-05-25T13:45:00Z,1,GSM3155122,peripheral blood mononuclear cells,SRP148992 +SRR7219409,OTHER,249,1733409794,PRJNA473147,SAMN09261101,744204103,CD8-enriched,GEO,154897,RPHERNGFTVL,positive,public,"fastq,sra,run.zq","ncbi,s3,gs","gs.us-east1,s3.us-east-1,ncbi.public",SRX4125957,GSM3155123,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,6471832,2018-11-23T00:00:00Z,2018-05-25T13:41:00Z,1,GSM3155123,peripheral blood mononuclear cells,SRP148992 +SRR7219410,OTHER,249,1451743817,PRJNA473147,SAMN09261100,601640922,CD8-enriched,GEO,119764,TPRVTGGGAM,positive,public,"fastq,run.zq,sra","ncbi,gs,s3","gs.us-east1,ncbi.public,s3.us-east-1",SRX4125958,GSM3155124,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,5359364,2018-11-23T00:00:00Z,2018-05-25T13:41:00Z,1,GSM3155124,peripheral blood mononuclear cells,SRP148992 +SRR7219411,OTHER,249,1952082056,PRJNA473147,SAMN09261099,813115105,CD8-enriched,GEO,111989,none,positive,public,"fastq,sra,run.zq","s3,ncbi,gs","s3.us-east-1,gs.us-east1,ncbi.public",SRX4125959,GSM3155125,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,7334612,2018-11-23T00:00:00Z,2018-05-25T13:44:00Z,1,GSM3155125,peripheral blood mononuclear cells,SRP148992 +SRR7219412,OTHER,249,1799947472,PRJNA473147,SAMN09261098,761139633,CD8-enriched,GEO,92462,CRVLCCYVL,positive,public,"sra,fastq,run.zq","gs,ncbi,s3","ncbi.public,s3.us-east-1,gs.us-east1",SRX4125960,GSM3155126,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,6748656,2018-11-23T00:00:00Z,2018-05-25T13:42:00Z,1,GSM3155126,peripheral blood mononuclear cells,SRP148992 +SRR7219413,OTHER,249,1615923876,PRJNA473147,SAMN09261097,602364308,CD8-enriched,GEO,21546,FRCPRRFCF,positive,public,"sra,fastq,run.zq","gs,s3,ncbi","ncbi.public,gs.us-east1,s3.us-east-1",SRX4125961,GSM3155127,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,6042090,2018-11-23T00:00:00Z,2018-05-25T13:41:00Z,1,GSM3155127,peripheral blood mononuclear cells,SRP148992 +SRR7219414,OTHER,249,1698311538,PRJNA473147,SAMN09261096,725727489,CD8-enriched,GEO,53741,RPHERNGFTVL,positive,public,"sra,run.zq,fastq","s3,ncbi,gs","s3.us-east-1,ncbi.public,gs.us-east1",SRX4125962,GSM3155128,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,6210355,2018-11-23T00:00:00Z,2018-05-25T13:44:00Z,1,GSM3155128,peripheral blood mononuclear cells,SRP148992 +SRR7219415,OTHER,249,1950299462,PRJNA473147,SAMN09261095,817643505,CD8-enriched,GEO,77073,TPRVTGGGAM,positive,public,"run.zq,fastq,sra","gs,ncbi,s3","s3.us-east-1,ncbi.public,gs.us-east1",SRX4125963,GSM3155129,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,7362160,2018-11-23T00:00:00Z,2018-05-25T13:43:00Z,1,GSM3155129,peripheral blood mononuclear cells,SRP148992 +SRR7219416,OTHER,396,7972070688,PRJNA473147,SAMN09261094,4402283858,unsorted,GEO,298620,none,positive,public,"sra,fastq,run.zq","s3,gs,ncbi","s3.us-east-1,gs.us-east1,ncbi.public",SRX4125964,GSM3155130,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,18297841,2018-11-23T00:00:00Z,2018-05-25T13:57:00Z,1,GSM3155130,peripheral blood mononuclear cells,SRP148992 +SRR7219417,OTHER,299,1527700770,PRJNA473147,SAMN09261093,824742609,unsorted,GEO,338203,none,positive,public,"fastq,run.zq,sra","ncbi,s3,gs","s3.us-east-1,gs.us-east1,ncbi.public",SRX4125965,GSM3155131,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,4627821,2018-11-23T00:00:00Z,2018-05-25T13:43:00Z,1,GSM3155131,peripheral blood mononuclear cells,SRP148992 +SRR7219418,OTHER,299,1587333214,PRJNA473147,SAMN09261092,859702187,unsorted,GEO,349765,none,positive,public,"fastq,run.zq,sra","ncbi,gs,s3","ncbi.public,gs.us-east1,s3.us-east-1",SRX4125966,GSM3155132,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,4763898,2018-11-23T00:00:00Z,2018-05-25T13:42:00Z,1,GSM3155132,peripheral blood mononuclear cells,SRP148992 +SRR7219419,OTHER,299,1632965753,PRJNA473147,SAMN09261091,914962252,unsorted,GEO,151726,none,positive,public,"sra,run.zq,fastq","ncbi,s3,gs","gs.us-east1,s3.us-east-1,ncbi.public",SRX4125967,GSM3155133,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,4670862,2018-11-23T00:00:00Z,2018-05-25T13:42:00Z,1,GSM3155133,peripheral blood mononuclear cells,SRP148992 +SRR7219420,OTHER,149,1842198889,PRJNA473147,SAMN09261090,1030747150,unsorted,GEO,312519,none,positive,public,"run.zq,fastq,sra","s3,gs,ncbi","ncbi.public,gs.us-east1,s3.us-east-1",SRX4125968,GSM3155134,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,11215100,2018-11-23T00:00:00Z,2018-05-25T13:48:00Z,1,GSM3155134,peripheral blood mononuclear cells,SRP148992 +SRR7219421,OTHER,299,1344609347,PRJNA473147,SAMN09261089,745561598,unsorted,GEO,311782,none,positive,public,"run.zq,sra,fastq","ncbi,gs,s3","gs.us-east1,ncbi.public,s3.us-east-1",SRX4125969,GSM3155135,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,3973821,2018-11-23T00:00:00Z,2018-05-25T13:43:00Z,1,GSM3155135,peripheral blood mononuclear cells,SRP148992 +SRR7219422,OTHER,299,3882443676,PRJNA473147,SAMN09261088,2107899083,unsorted,GEO,103645,none,positive,public,"run.zq,fastq,sra","gs,s3,ncbi","s3.us-east-1,ncbi.public,gs.us-east1",SRX4125970,GSM3155136,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,11695158,2018-11-23T00:00:00Z,2018-05-25T13:52:00Z,1,GSM3155136,peripheral blood mononuclear cells,SRP148992 +SRR7219423,OTHER,299,1482582550,PRJNA473147,SAMN09261087,824638039,unsorted,GEO,201133,none,positive,public,"fastq,sra,run.zq","gs,ncbi,s3","gs.us-east1,ncbi.public,s3.us-east-1",SRX4125971,GSM3155137,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,4380130,2018-11-23T00:00:00Z,2018-05-25T13:41:00Z,1,GSM3155137,peripheral blood mononuclear cells,SRP148992 +SRR7219424,OTHER,299,1908822438,PRJNA473147,SAMN09261086,1054104816,unsorted,GEO,163397,none,positive,public,"fastq,sra,run.zq","ncbi,gs,s3","ncbi.public,s3.us-east-1,gs.us-east1",SRX4125972,GSM3155138,Illumina HiSeq 1500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,5679983,2018-11-23T00:00:00Z,2018-05-25T13:42:00Z,1,GSM3155138,peripheral blood mononuclear cells,SRP148992 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b/man/Motif-class.Rd index 59dac4e..43e3695 100644 --- a/man/Motif-class.Rd +++ b/man/Motif-class.Rd @@ -10,10 +10,12 @@ A class to represent motif metrics \section{Slots}{ \describe{ -\item{\code{aa_spectratype}}{aa spectratype data} +\item{\code{aa_spectra}}{Amino acid spectratype} -\item{\code{aa_max_spectratype}}{aa max spectratype data} +\item{\code{aa_max_spectra}}{Amino acid max spectratype} -\item{\code{aa_motif_count}}{aa motif count data} +\item{\code{aa_motif_count}}{Amino acid motif count table} + +\item{\code{aa_most_motif}}{Most abundant amino acid motif per sample} }} diff --git a/man/get_study.Rd b/man/get_study.Rd index b3a4200..c18f278 100644 --- a/man/get_study.Rd +++ b/man/get_study.Rd @@ -19,6 +19,6 @@ Retrieve the pyTCR data of a project by its ID. } \examples{ \dontrun{ -proj <- reTCR::get_study(id = "PRJNA473147", attr_col = "cmv_status") +proj <- reTCR::get_study(id="PRJNA473147", attr_col="cmv_status") } } diff --git a/man/plot_motif_counts.Rd b/man/plot_motifs.Rd similarity index 62% rename from man/plot_motif_counts.Rd rename to man/plot_motifs.Rd index 21ab5a1..78b8e1f 100644 --- a/man/plot_motif_counts.Rd +++ b/man/plot_motifs.Rd @@ -1,15 +1,17 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/utils-motif-plot.R -\name{plot_motif_counts} -\alias{plot_motif_counts} +\name{plot_motifs} +\alias{plot_motifs} \title{Plot Motif Counts} \usage{ -plot_motif_counts(data, threshold = 60) +plot_motifs(data, attr_col, k = 60) } \arguments{ \item{data}{A data frame containing the motif counts.} -\item{threshold}{the minimum count threshold (default: 60).} +\item{attr_col}{Character. Attribute column name.} + +\item{k}{the minimum count threshold (default: 60).} } \value{ A ggplot2 object representing the motif counts plot. @@ -20,6 +22,6 @@ This function plots the motif counts. \examples{ \dontrun{ proj <- reTCR::get_study(id="PRJNA473147", attr_col="cmv_status") -reTCR::plot_motif_counts(proj@motif@aa_motif_count, 20) +reTCR::plot_motifs(proj@motif@aa_motif_count, "cmv_status", 50) } } diff --git a/man/reTCRProj-class.Rd b/man/reTCRProj-class.Rd index c5d5fc0..7253bff 100644 --- a/man/reTCRProj-class.Rd +++ b/man/reTCRProj-class.Rd @@ -10,7 +10,9 @@ A class to represent a reTCR project \section{Slots}{ \describe{ -\item{\code{data}}{contains the main data for the project} +\item{\code{data}}{contains the MIXCR data for the project} + +\item{\code{metadata}}{contains the sample metadata} \item{\code{basic}}{contains basic metrics} @@ -18,6 +20,8 @@ A class to represent a reTCR project \item{\code{clonality}}{contains clonality metrics} +\item{\code{motif}}{contains motif metrics} + \item{\code{hill}}{contains Hill numbers} }}