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% Generated by roxygen2: do not edit by hand |
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% Please edit documentation in R/CircosFruits.R |
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\name{circos_fruits} |
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\alias{circos_fruits} |
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\title{Add multiple layers to a `ggtree` plot for visualizing gene expression and enrichment data} |
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\usage{ |
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circos_fruits( |
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p, |
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long_format_HeatdataDeseq, |
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ssgsea_kegg_HeatdataDeseq, |
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gsva_kegg_HeatdataDeseq, |
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gene_colors |
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) |
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} |
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\arguments{ |
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\item{p}{A `ggtree` plot object to which the data and layers will be added.} |
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\item{long_format_HeatdataDeseq}{A data frame containing gene expression data with columns for `Samples`, `Genes`, and `Values`.} |
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\item{ssgsea_kegg_HeatdataDeseq}{A data frame containing SSGSEA analysis results with columns for `Samples`, `Genes`, and `Values`.} |
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\item{gsva_kegg_HeatdataDeseq}{A data frame containing GSVA analysis results with columns for `Samples`, `Genes`, and `Values`.} |
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\item{gene_colors}{A named vector of colors for genes, used for coloring tiles in different layers.} |
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} |
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\value{ |
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A `ggtree` plot object with multiple layers added for comprehensive visualization. |
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} |
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\description{ |
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This function sequentially adds multiple layers to a `ggtree` plot, including gene expression data, boxplots for statistical |
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summaries, and additional tile layers for pathway enrichment scores from SSGSEA and GSVA analyses. It utilizes separate |
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functions for adding each type of layer and allows for the specification of gene colors as well as adjustments in aesthetics |
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for each layer. The function is designed to work with specific data structures and assumes all functions for adding layers |
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are defined and available. |
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} |
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\examples{ |
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\donttest{ |
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# Check and load required packages |
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if (requireNamespace("ggtreeExtra", quietly = TRUE) && |
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requireNamespace("ggplot2", quietly = TRUE)) { |
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library(ggtreeExtra) |
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library(ggplot2) |
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# Example data for gene expression, SSGSEA, and GSVA |
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file_path <- system.file("extdata", "p_tree_test.rds", package = "TransProR") |
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p <- readRDS(file_path) |
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# Create gene expression data frame (long_format_HeatdataDeseq) |
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long_format_HeatdataDeseq <- data.frame( |
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Sample = rep(c("Species_A", "Species_B", "Species_C", "Species_D"), each = 5), |
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Genes = rep(paste0("Gene", 1:5), times = 4), |
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Value = runif(20, min = 0, max = 1) # Randomly generate expression values between 0 and 1 |
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) |
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# Create SSGSEA analysis results data frame (ssgsea_kegg_HeatdataDeseq) |
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ssgsea_kegg_HeatdataDeseq <- data.frame( |
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Sample = rep(c("Species_A", "Species_B", "Species_C", "Species_D"), each = 3), |
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Genes = rep(c("Pathway1", "Pathway2", "Pathway3"), times = 4), |
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Value = runif(12, min = 0, max = 1) # Randomly generate enrichment scores between 0 and 1 |
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) |
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# Create GSVA analysis results data frame (gsva_kegg_HeatdataDeseq) |
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gsva_kegg_HeatdataDeseq <- data.frame( |
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Sample = rep(c("Species_A", "Species_B", "Species_C", "Species_D"), each = 4), |
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Genes = rep(c("PathwayA", "PathwayB", "PathwayC", "PathwayD"), times = 4), |
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Value = runif(16, min = 0, max = 1) # Randomly generate enrichment scores between 0 and 1 |
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) |
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# Define gene and pathway colors (named vector), including all genes and pathways |
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gene_colors <- c( |
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# Genes for gene expression |
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Gene1 = "#491588", |
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Gene2 = "#301b8d", |
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Gene3 = "#1a237a", |
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Gene4 = "#11479c", |
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Gene5 = "#0a5797", |
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# Pathways for SSGSEA |
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Pathway1 = "#0b5f63", |
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Pathway2 = "#074d41", |
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Pathway3 = "#1f5e27", |
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# Pathways for GSVA |
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PathwayA = "#366928", |
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PathwayB = "#827729", |
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PathwayC = "#a1d99b", |
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PathwayD = "#c7e9c0" |
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) |
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# Call circos_fruits function to add multiple layers |
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final_plot <- circos_fruits( |
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p, |
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long_format_HeatdataDeseq, |
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ssgsea_kegg_HeatdataDeseq, |
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gsva_kegg_HeatdataDeseq, |
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gene_colors |
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) |
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} else { |
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message("Required packages 'ggtreeExtra' and 'ggplot2' are not installed.") |
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} |
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} |
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} |