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default asEnrichdat to enrichment analysis
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,124 @@ | ||
| #' Adjust dataframe for enrichment plot | ||
| #' | ||
| #' make sure colname contains Description, Count, FoldEnrich/GeneRatio, pvalue/qvalue/p.adjust | ||
| #' | ||
| #' @param enrich_df dataframe of enrichment analysis result . | ||
| #' | ||
| #' @importFrom stringr str_remove_all str_split str_remove | ||
| #' @importFrom dplyr mutate pull | ||
| #' @return A `data.frame`. | ||
| #' @export | ||
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| as.enrichdat <- function(enrich_df) { | ||
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| ## get lower case colnames | ||
| remove <- c("\\(", "\\)", " ", "-", "_") | ||
| to_check <- stringr::str_remove_all(tolower(colnames(enrich_df)), paste(remove, collapse = "|")) | ||
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| ## find description col | ||
| if (!any(grepl("description", to_check))) { | ||
| check_description <- apply(enrich_df, 2, function(x) all(grepl("[A-Za-z]{3,}", x))) | ||
| check2 <- which(check_description) | ||
| if (any(check2 < (ncol(enrich_df) / 2))) { | ||
| colnames(enrich_df)[check_description][check2 < 5] <- "Description" | ||
| } else { | ||
| stop("Not found description column!") | ||
| } | ||
| } else { | ||
| colnames(enrich_df)[grepl("description", to_check)] <- "Description" | ||
| } | ||
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| ## find count col | ||
| # if finds genes col, calc gene num as count; else find another col as count | ||
| if (!any(grepl("count", to_check))) { | ||
| check_gene <- apply(enrich_df, 2, function(x) all(grepl("[A-Za-z]{3,}|\\/|,", x) & !grepl("tags|list", x))) | ||
| check2 <- which(check_gene) | ||
| if (any(check2 > (ncol(enrich_df) / 2))) { | ||
| colnames(enrich_df)[check_gene][check2 > (ncol(enrich_df) / 2)] <- "geneID" | ||
| gen_num <- stringr::str_split(enrich_df$geneID, ",|\\/") %>% | ||
| lapply(., length) %>% | ||
| unlist() | ||
| enrich_df <- enrich_df %>% dplyr::mutate(Count = gen_num) | ||
| } else if (any(grepl("\\([1-9]{,4}\\)", colnames(enrich_df)))) { | ||
| gen_num <- enrich_df[grepl("\\([1-9]{,4}\\)", colnames(enrich_df))] %>% | ||
| dplyr::pull(1) %>% | ||
| as.numeric() | ||
| enrich_df <- enrich_df %>% dplyr::mutate(Count = gen_num) | ||
| } else { | ||
| stop('Please rename the gene count column as "Count"!') | ||
| # head(enrich_df[1:2,]) | ||
| # message("Cannot auto-select count column...","\n","Please specify the column number which includes gene count...") | ||
| # answer <- scan(what = "character", n =1,quiet =T) | ||
| # message('Choose the No. ',answer,' column as gene count...') | ||
| # enrich_df = enrich_df %>% dplyr::rename(Count = eval(parse(text = answer))) | ||
| } | ||
| } else { | ||
| colnames(enrich_df)[grepl("count", to_check)] <- "Count" | ||
| } | ||
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| ## find FoldEnrich col | ||
| # GSEA result has no FoldEnrich, need to exclude | ||
| if (!(any(grepl("\\benrichmentscore\\b", to_check)) & any(grepl("\\bleadingedge\\b", to_check)))) { | ||
| if (any(grepl("foldenrich|enrichment", to_check))) { | ||
| colnames(enrich_df)[grepl("foldenrich|enrichment", to_check)] <- "FoldEnrich" | ||
| } else { | ||
| stop('Please rename the fold enrichment column as "FoldEnrich"!') | ||
| # head(enrich_df[1:2,]) | ||
| # message("Cannot auto-select fold enrichment column...","\n", | ||
| # "Please specify the column number which includes fold enrichment...") | ||
| # answer <- scan(what = "character", n =1,quiet =T) | ||
| # message('Choose the No. ',answer,' column as fold enrichment...') | ||
| # enrich_df = enrich_df %>% dplyr::rename(FoldEnrich = eval(parse(text = answer))) | ||
| } | ||
| } | ||
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| ## find GeneRatio col | ||
| if (any(grepl("generatio", to_check))) { | ||
| colnames(enrich_df)[grepl("generatio", to_check)] <- "GeneRatio" | ||
| enrich_df <- enrich_df %>% dplyr::mutate(GeneRatio = sapply(.$GeneRatio, function(x) eval(parse(text = x)))) | ||
| } else { | ||
| # gsea | ||
| if (any(grepl("setsize", to_check))) { | ||
| colnames(enrich_df)[grepl("setsize", to_check)] <- "setSize" | ||
| enrich_df <- enrich_df %>% dplyr::mutate(GeneRatio = as.numeric(Count) / as.numeric(setSize)) | ||
| } else if (any(grepl("\\([1-9]{,4}\\)", colnames(enrich_df)))) { | ||
| # panther result | ||
| setsize <- colnames(enrich_df)[grepl("\\([1-9]{,4}\\)", colnames(enrich_df))] %>% | ||
| stringr::str_remove(., ".*\\(") %>% | ||
| stringr::str_remove(., "\\)") %>% | ||
| as.numeric() | ||
| enrich_df <- enrich_df %>% dplyr::mutate(GeneRatio = as.numeric(Count) / setsize) | ||
| } else if (apply(enrich_df, 2, function(x) length(unique(x)) == 1)) { | ||
| setsize <- enrich_df[1, apply(enrich_df, 2, function(x) length(unique(x)) == 1)] %>% | ||
| stringr::str_remove("0") %>% | ||
| as.numeric() %>% | ||
| sort() %>% | ||
| .[1] | ||
| enrich_df <- enrich_df %>% dplyr::mutate(GeneRatio = as.numeric(Count) / setsize) | ||
| } | ||
| } | ||
|
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| ## find pvalue col | ||
| if (any(grepl("pvalue", to_check))) { | ||
| colnames(enrich_df)[grepl("pvalue", to_check)] <- "pvalue" | ||
| } else if (any(grepl("\\buncorrectedpvalue\\b", to_check))) { | ||
| colnames(enrich_df)[grepl("\\buncorrectedpvalue\\b", to_check)] <- "pvalue" | ||
| } | ||
|
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| ## find p.adjust col | ||
| if (any(grepl("p.adjust", to_check))) { | ||
| colnames(enrich_df)[grepl("p.adjust", to_check)] <- "p.adjust" | ||
| } else if (any(grepl("\\bcorrectedpvalue\\b", to_check))) { | ||
| colnames(enrich_df)[grepl("\\bcorrectedpvalue\\b", to_check)] <- "p.adjust" | ||
| } | ||
|
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| ## find qvalue col | ||
| if (any(grepl("qvalue", to_check))) { | ||
| colnames(enrich_df)[grepl("qvalue", to_check)] <- "qvalue" | ||
| } else if (any(grepl("fdr", to_check) & !grepl("fdrrate", to_check))) { | ||
| colnames(enrich_df)[grepl("fdr", to_check)] <- "qvalue" | ||
| } | ||
|
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||
| return(enrich_df) | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -248,3 +248,4 @@ calcFoldEnrich <- function(df) { | |
| } | ||
| return(df) | ||
| } | ||
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