Gene ranking dotplot for visualizing differentailly expressed genes.

Usage

gene_rank_plot(
  data,
  log2fc = 1,
  palette = "Spectral",
  top_n = 10,
  genes_to_label = NULL,
  label_size = 5,
  base_size = 12,
  title = "Gene ranking dotplot",
  xlab = "Ranking of differentially expressed genes",
  ylab = "Log2FoldChange"
)

Arguments

data: Dataframe: All DEGs of paired comparison CT-vs-LT12 stats dataframe (1st-col: Genes, 2nd-col: log2FoldChange, 3rd-col: Pvalue, 4th-col: FDR).
log2fc: Numeric: log2(FoldChange) cutoff log2(2) = 1. Default: 1.0, min: 0.0, max: null.
palette: Character: color palette used for the point. Default: "spectral", options: 'Spectral', 'BrBG', 'PiYG', 'PRGn', 'PuOr', 'RdBu', 'RdGy', 'RdYlBu', 'RdYlGn'.
top_n: Numeric: number of top differentailly expressed genes. Default: 10, min: 0.
genes_to_label: Character: a vector of selected genes. Default: "NULL".
label_size: Numeric: gene label size. Default: 5, min: 0.
base_size: Numeric: base font size. Default: 12, min: 0.
title: Character: main plot title. Default: "Gene ranking dotplot".
xlab: Character: title of the xlab. Default: "Ranking of differentially expressed genes".
ylab: Character: title of the ylab. Default: "Log2FoldChange".

Value

Plot: Gene ranking dotplot for visualizing differentailly expressed genes.

Author

wei dong

Examples

# 1. Library TOmicsVis package
library(TOmicsVis)

# 2. Use example dataset
data(degs_stats)
head(degs_stats)
#>    Gene log2FoldChange      Pvalue         FDR
#> 1  A1I3    -1.13855748 0.000111040 0.000862478
#> 2   A1M     0.59076131 0.070988041 0.192551708
#> 3   A2M     0.09297827 0.819706797 0.913893947
#> 4 A2ML1    -0.26940689 0.745374782 0.874295125
#> 5  ABAT     1.24811621 0.000001440 0.000016800
#> 6 ABCC3    -0.72947545 0.005171574 0.024228298

# 3. Default parameters
gene_rank_plot(degs_stats)


# 4. Set top_n = 5
gene_rank_plot(degs_stats, top_n = 5, palette = "PiYG")


# 5. Set genes_to_label = c("SELL","CCR7","KLRG1","IL7R")
gene_rank_plot(degs_stats, genes_to_label = c("SELL","CCR7","KLRG1","IL7R"), palette = "PuOr")
#> Warning: Removed 4 rows containing missing values (`geom_text_repel()`).