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% Generated by roxygen2: do not edit by hand |
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% Please edit documentation in R/MergeDensityFoldchange.R |
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\name{merge_density_foldchange} |
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\alias{merge_density_foldchange} |
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\title{Create high-density region plot with optional points, density rugs, and contours} |
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\usage{ |
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merge_density_foldchange( |
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data, |
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x_var, |
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y_var, |
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group_var, |
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palette = c("#3949ab", "#1e88e5", "#039be5", "#00897b", "#43a047", "#7cb342"), |
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show_points = FALSE, |
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point_size = 2.5, |
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point_alpha = 0.2, |
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x_lim = c(0, 20), |
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y_lim = c(0, 20), |
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cor_method = "pearson", |
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line_size = 1.6, |
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cor_label_pos = c("left", 0.97) |
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) |
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} |
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\arguments{ |
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\item{data}{Data frame containing variables for plotting.} |
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\item{x_var}{Name of the x-axis variable as a string.} |
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\item{y_var}{Name of the y-axis variable as a string.} |
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\item{group_var}{Name of the grouping variable for color mapping as a string.} |
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\item{palette}{Color palette for the plot as a character vector.} |
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\item{show_points}{Logical, if TRUE adds points to the plot.} |
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\item{point_size}{Size of the points, relevant if show_points is TRUE.} |
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\item{point_alpha}{Transparency level of the points, relevant if show_points is TRUE.} |
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\item{x_lim}{Numeric vector of length 2, giving the x-axis limits.} |
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\item{y_lim}{Numeric vector of length 2, giving the y-axis limits.} |
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\item{cor_method}{Method to calculate correlation ("pearson" or "spearman").} |
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\item{line_size}{Size of the smoothing line.} |
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\item{cor_label_pos}{Vector of length 2 indicating the position of the correlation label (x and y).} |
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} |
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\value{ |
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A ggplot object representing the high-density region plot. |
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} |
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\description{ |
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This function creates a high-density region plot using hdr methods to |
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add density rug and filled contours. It also adds a regression line |
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and Pearson correlation label. Points can be added to the plot optionally. |
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} |
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\examples{ |
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combined_df_file <- system.file("extdata", "combined_df.rds", package = "TransProR") |
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combined_df <- readRDS(combined_df_file) |
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pal1 = c("#3949ab","#1e88e5","#039be5","#00897b","#43a047","#7cb342") |
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all_density_foldchange_name1 <- merge_density_foldchange( |
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data = combined_df, |
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x_var = "log2FoldChange_1", |
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y_var = "log2FoldChange_2", |
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group_var = "name", |
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palette = pal1, |
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show_points = FALSE, |
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point_size = 2.5, |
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point_alpha = 0.1, |
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x_lim = c(0, 20), |
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y_lim = c(0, 20), |
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cor_method = "pearson", |
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line_size = 1.6, |
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cor_label_pos = c("left", "top") |
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) |
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} |