Plot Log2 Fold-Change Results for Selected Genes

Creates a bar plot of log2 fold-change values for transcripts of a selected gene, differentiating transcript types and significance levels.

Usage

plot_log2FC(DEG_DET_table, selected_gene, custom_colors = NULL)

Arguments

DEG_DET_table: A data.frame or tibble containing combined gene and transcript differential expression results, including name, log2FC, transcript_type, significance, and gene_name columns.
selected_gene: A character string specifying the gene name to plot.
custom_colors: An optional named vector of colors for different transcript types.

Value

A ggplot2 object representing the bar plot.

Details

The function filters the input table for the selected gene and creates a bar plot of log2 fold-change values. If all transcripts are significant, it plots without adjusting alpha transparency; otherwise, it adjusts alpha based on significance. The function uses predefined colors for transcript types, which can be overridden by providing custom_colors.

Examples

# Sample data
DEGs_DETs_table <- data.frame(
  name = c("Transcript1", "Transcript2", "GeneA"),
  log2FC = c(1.5, -2.0, 0.8),
  transcript_type = c("protein_coding", "lncRNA", "gene"),
  significance = c("sig", "not_sig", "sig"),
  gene_name = c("GeneA", "GeneA", "GeneA")
)

# Plot log2 fold-change for the selected gene
plot_obj <- plot_log2FC(
  DEG_DET_table = DEGs_DETs_table,
  selected_gene = "GeneA"
)
#> Error in plot_log2FC(DEG_DET_table = DEGs_DETs_table, selected_gene = "GeneA"): object 'tx_type_color_names' not found

# Display the plot
print(plot_obj)
#> Error: object 'plot_obj' not found