plot_deg_scatter: Scatter plot of the comparison groups

In espors/idepGolem: Integrated Differential Expression and Pathway Analysis

Scatter plot of the comparison groups

Description

Create a scatter plot of the expression value for each gene in the two groups for the selected contrast. For the selected contrast, the mean expression is calculated for a gene in both group of samples in the contrast and plotted in a scatter plot.

Usage

plot_deg_scatter(
  select_contrast,
  comparisons,
  top_genes,
  limma_p_val,
  limma_fc,
  contrast_samples,
  processed_data,
  sample_info,
  plot_colors,
  all_gene_names,
  anotate_genes = NULL
)

Arguments

select_contrast	Comparison from DEG analysis to filter for the significant genes
comparisons	The comparisons vector from the results list of the limma_value function
top_genes	top_genes list from results list of the limma_value function
limma_p_val	Significant p-value to use to in determining the expressed genes
limma_fc	Minimum fold change value to use in determining the expressed genes
contrast_samples	Samples that are included in the selected comparison
processed_data	Data matrix that has gone through pre-processing
sample_info	Experiment file information for grouping
plot_colors	List containing three colors to differentiate between the up-regulated, down-regulated, and other genes
anotate_genes	Genes to be anotated, coming from mod_label_server()
vol_data	Volcano data used in gene annotation

Value

A formatted ggplot with the X-axis as the mean expression of one contrast group and the Y-axis as the mean expression of the other contrast group.

espors/idepGolem documentation built on April 23, 2024, 1:11 p.m.