jj_plot_volcano: show results from differential expression analysis

In mathosi/jj: Just Joise

show results from differential expression analysis

Description

jj_plot_volcano volcano plot of pval (which is -log10 transformed) against logFC

Usage

jj_plot_volcano(
  plot_df,
  logfc_column,
  pval_column,
  symbol_column = NULL,
  marker_thres = c(0.5, Inf),
  labs_range = NULL,
  alpha = 1,
  pt.size = 2.5,
  highlight.pt.size = 2.5,
  col_vec = c("red", "blue", "black", "green"),
  markers_highlight = NULL,
  markers_highlight_col = NULL,
  only_highlight = FALSE,
  col_by_highlight = FALSE,
  use_text = TRUE,
  add_thres_line = FALSE,
  group_names = NULL,
  arrow_pos = list(x = 0.25, xend = 1, y = 40)
)

Arguments

logfc_column	sparse matrix, vector, or data.frame
pval_column	vector with group annotation, has to have length equal to ncol(sparse_mat)/nrow(data.frame)/length(vector)
symbol_column	provide symbol_column to add text to all points that are highlighted (when use_text=TRUE)
marker_thres	define marker_thres to highlight all points with absolute value above
labs_range	vector specifying range of x axis (and for fc_fc plot range of y axis)
alpha	alpha level for points (working?)
col_vec	define larger, smaller, intermediate and highlight colours
markers_highlight	vector of genes from the symbol_column which should additionally be highlighted
markers_highlight_col	named vector assigning a colour to each gene to be highlighed
only_highlight	if TRUE, only show markers specified in markers_highlight
col_by_highlight	if TRUE, only colour the markers specified in markers_highlight
use_text	plot text if there are any points to highlight
add_thres_line	if TRUE, plot dashed lines at the defined marker_thres

Value

ggplot scatterplot of log10(pval) vs FC or FC vs FC

Examples

#Using Seurats FindMarkers output
library(Seurat)
marker_df = FindMarkers(pbmc_small, group.by = 'groups', ident.1 = 'g1', ident.2 = 'g2')
marker_df$symbol = rownames(marker_df)
#or using a random data.frame
marker_df = data.frame(avg_log2FC = rnorm(100, 0, 2), 
p_val = sample(c(runif(50, 0, 0.1), runif(50))), 
symbol = paste0(sample(LETTERS, 100, replace = T), sample(letters, 100, replace = T), 1:100))
jj_plot_volcano(marker_df, logfc_column = 'avg_log2FC', pval_column = 'p_val', marker_thres = Inf) + theme(legend.position = 'none')
#colour highlighting above a threshold and capping very high and low values, adding lines for the threshold
jj_plot_volcano(marker_df, logfc_column = 'avg_log2FC', pval_column = 'p_val',
 labs_range = c(-2,2), marker_thres = 1.5, add_thres_line=T)
#adding text to highlighted markers, possibility to show unbalanced x axis
jj_plot_volcano(marker_df, logfc_column = 'avg_log2FC', pval_column = 'p_val', symbol_column = 'symbol', 
use_text = T, labs_range = c(-2,4), marker_thres = 2)
#instead of highlighting everything above/below a threshold, specific markers can be highlighted
jj_plot_volcano(marker_df, logfc_column = 'avg_log2FC', pval_column = 'p_val', symbol_column = 'symbol',
               labs_range = c(-2.5, 2.5), marker_thres = 4,
               markers_highlight = marker_df$symbol[1:4], pt.size = 1.5,
               only_highlight = F, col_by_highlight = T)
#specific highlighting and general highlighting can be combined
jj_plot_volcano(marker_df, logfc_column = 'avg_log2FC', pval_column = 'p_val', symbol_column = 'symbol',
               labs_range = c(-2.5, 2.5), marker_thres = 2,
               markers_highlight = marker_df$symbol[1:4], pt.size = 1.5, highlight.pt.size = 3,
               only_highlight = F, col_by_highlight = F)
#only show highlighted markers
jj_plot_volcano(marker_df, logfc_column = 'avg_log2FC', pval_column = 'p_val', symbol_column = 'symbol',
               labs_range = c(-2.5, 2.5), marker_thres = 2,
               markers_highlight =  marker_df$symbol[1:4], pt.size = 1.5, 
               only_highlight = T, col_by_highlight = F)
#to change colour and size of highlighted markers use `highlight.pt.size` and `markers_highlight_cols`                
jj_plot_volcano(marker_df, logfc_column = 'avg_log2FC', pval_column = 'p_val', symbol_column = 'symbol',
               labs_range = c(-4, 4), marker_thres = Inf,
               markers_highlight =  marker_df$symbol[1:4], pt.size = 1.5, highlight.pt.size = 3,
               only_highlight = F, col_by_highlight =T,
               markers_highlight_col = structure(c('red','orange','red','blue'), names = marker_df$symbol[1:4])) + theme(legend.position='none')

mathosi/jj documentation built on Feb. 25, 2024, 2:29 p.m.