chromosome_plotly: Plotly of chromosome position

In espors/idepGolem: Integrated Differential Expression and Pathway Analysis

Plotly of chromosome position

Description

Calculate a plotly that shows the chromosome position of significant genes and significantly enriched regions.

Usage

chromosome_plotly(
  limma,
  select_contrast,
  all_gene_info,
  ignore_non_coding,
  limma_p_val_viz,
  limma_fc_viz,
  label_gene_symbol,
  ma_window_size,
  ma_window_steps,
  ch_region_p_val,
  hide_patches,
  hide_chr
)

Arguments

limma	Return from limma_value function
select_contrast	DEG contrast to examine
all_gene_info	Gene information return from get_gene_info
ignore_non_coding	When TRUE only use protein coding genes
limma_p_val_viz	Adjusted p-value to use for significant genes
limma_fc_viz	Minimum fold-change value to filter with
label_gene_symbol	Paste the gene symbol label on the plot
ma_window_size	Moving average window size for a chromosome (1, 2, 4, 6, 8, 10, 15, 20)
ma_window_steps	Number of moving average window steps (1, 2, 3, 4)
ch_region_p_val	P-value to use for finding significant chromosome region enrichment
hide_patches	Boolean to indicate to only keep within 2 MAD from the median (TRUE/FALSE)
hide_chr	Boolean to indicate if chromosomes with less than 100 genes are excluded (TRUE/FALSE)

Value

Plotly visualization of chromosomes and significantly enriched genes

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