forked from openbiox/UCSCXenaShiny
-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request openbiox#337 from lishensuo/master
improve UI of TPC modules
- Loading branch information
Showing
28 changed files
with
218 additions
and
52 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,106 @@ | ||
| #' Visualize Correlation between Gene and Pathway signature Score | ||
| #' @param Gene a molecular identifier (e.g., "TP53") or a formula | ||
| #' specifying genomic signature ("TP53 + 2 * KRAS - 1.3 * PTEN"). | ||
| #' @param data_type choose gene profile type, including | ||
| #' "mRNA", "transcript", "protein", "mutation", "cnv", "methylation", "miRNA". | ||
| #' @param pw_name the queried Pathway name, see the supported pathway from 'load("toil_sig_score")'default is NULL | ||
| #' @param cancer_choose select cancer cohort(s) | ||
| #' @param use_regline if TRUE, add regression line. | ||
| #' @param cor_method select correlation coefficient (pearson/spearman) | ||
| #' @param use_all use all sample, default FALSE. | ||
| #' @param alpha dot alpha. | ||
| #' @param color dot color. | ||
| #' @param filter_tumor whether use tumor sample only, default TRUE | ||
| #' @param opt_pancan specify one dataset for some molercular profiles | ||
|
|
||
| #' @return a `ggplot` object or dataframe | ||
| #' @examples | ||
| #' \dontrun{ | ||
| #' vis_gene_pw_cor(Gene = "TP53", data_type = "mRNA", | ||
| #' pw_name = "HALLMARK_ADIPOGENESIS", | ||
| #' cancer_choose = "BRCA") | ||
| #' } | ||
|
|
||
| #' @export | ||
| #' | ||
| vis_gene_pw_cor <- function(Gene = "TP53", | ||
| data_type = "mRNA", | ||
| pw_name = "HALLMARK_ADIPOGENESIS", | ||
| cancer_choose = "GBM", | ||
| use_regline = TRUE, | ||
| cor_method = "spearman", | ||
| use_all = FALSE, | ||
| alpha = 0.5, | ||
| color = "#000000", | ||
| filter_tumor = TRUE, | ||
| opt_pancan = .opt_pancan){ | ||
| if (!file.exists(file.path(get_zenodo_dir(), "tcga_PW.rda"))) { | ||
| print("This is the first download from zenodo, please wait a few minutes.") | ||
| } | ||
| toil_sig_score <- load_data("tcga_PW") | ||
| toil_sig_meta <- load_data("tcga_PW_meta") | ||
| if (!is.null(pw_name)) { | ||
| if (!(pw_name %in% toil_sig_meta$ID)) { | ||
| stop("You need provide valid pathway name (see load_data('tcga_PW_meta'))") | ||
| } | ||
| } | ||
| # gene expression | ||
| t1 <- query_pancan_value(Gene, data_type = data_type, opt_pancan = opt_pancan) | ||
| if (is.null(t1[[1]])) { | ||
| warning("No data available", immediate. = TRUE) | ||
| return(NULL) | ||
| } | ||
| if (is.list(t1)) t1 <- t1[[1]] | ||
| if (all(is.na(t1))) { | ||
| message("All NAs returned, return NULL instead.") | ||
| return(NULL) | ||
| } | ||
| message(paste0("Get data value for ", Gene)) | ||
| s <- data.frame(Sample = names(t1), values = t1) | ||
|
|
||
|
|
||
| # message("Mode-3: one specific pathway correlated to one specific cancer") | ||
| toil_sig_score <- load_data("tcga_PW") | ||
|
|
||
| tcga_gtex <- load_data("tcga_gtex") | ||
| if(use_all){ | ||
| cancer_choose2 = as.character(unique(tcga_gtex$tissue)) | ||
| } else { | ||
| cancer_choose2 = cancer_choose | ||
| } | ||
| if(filter_tumor){ | ||
| filter_tumor2 = 'tumor' | ||
| } else { | ||
| filter_tumor2 = c('tumor','normal') | ||
| } | ||
| tcga_sp <- tcga_gtex %>% | ||
| dplyr::filter(.data$type2 == filter_tumor2) %>% | ||
| dplyr::filter(.data$tissue %in% cancer_choose2) %>% | ||
| dplyr::pull(sample) %>% | ||
| as.character() | ||
|
|
||
| res_pan_spe <- toil_sig_score[rownames(toil_sig_score) %in% tcga_sp, pw_name, drop = F] %>% | ||
| as.data.frame() %>% tibble::rownames_to_column("Sample") %>% | ||
| tidyr::pivot_longer(!"Sample", names_to = "pw_name", values_to = "pw_score") %>% | ||
| dplyr::left_join(s) %>% | ||
| dplyr::mutate(identifier = Gene, .before = 1) %>% | ||
| dplyr::mutate(Cancer = tcga_gtex$tissue[match(.data$Sample, tcga_gtex$sample)], .before = 3) %>% | ||
| tibble() | ||
|
|
||
| cor_res <- ezcor(data = as.data.frame(res_pan_spe), var1 = "values", var2 = "pw_score", cor_method = cor_method) | ||
| p <- ggplot2::ggplot(res_pan_spe, aes_string(x = "values", y = "pw_score")) + | ||
| ggplot2::geom_point(shape = 16, size = 3, show.legend = FALSE, alpha = alpha, color = color) + | ||
| ggplot2::theme_minimal() + | ||
| ggplot2::labs(x = paste(Gene, data_type), y = pw_name) + | ||
| ggplot2::annotate( | ||
| "text", | ||
| -Inf, Inf, | ||
| hjust = -0.1, vjust = 1, | ||
| label = paste0("Cor: ", round(cor_res$cor, 2), " ", cor_res$pstar), | ||
| size = 8, colour = "black" | ||
| ) | ||
|
|
||
| if (use_regline) p <- p + ggplot2::geom_smooth(method = stats::lm) | ||
|
|
||
| return(p) | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.