plot_expr_boxplot = function(expr_list_all, group_df, gene, p_group) sample_ids = group_df$Sample expr_list = lapply(sample_ids, function(x) expr_df = data.frame(expr_list_all[[x]][gene, ]) expr_df$Sample = x colnames(expr_df) = c("Gene", "Sample") return(expr_df) ) plot_df = do.call("rbind", expr_list) plot_df$Sample = factor(plot_df$Sample, levels = rev(sample_ids)) p <- ggplot(data=plot_df, aes(x=Sample, y=Gene)) + labs(y = gene) + # geom_bar(stat="identity") + geom_boxplot(fill='#A4A4A4') + scale_y_continuous(position = "right", expand = c(0,0)) + coord_flip() + ylim2(p_group) + theme( panel.background = element_rect(fill='transparent'), plot.background = element_rect(fill='transparent', color=NA), axis.text.y=element_blank(), axis.title.y=element_blank() ) return(p) Merge all plots together a large plot

plot_expr_boxplot = function(expr_list_all, group_df, gene, p_group) sample_ids = group_df$Sample expr_list = lapply(sample_ids, function(x) expr_df = data.frame(expr_list_all[[x]][gene, ]) expr_df$Sample = x colnames(expr_df) = c("Gene", "Sample") return(expr_df) ) plot_df = do.call("rbind", expr_list) plot_df$Sample = factor(plot_df$Sample, levels = rev(sample_ids)) p <- ggplot(data=plot_df, aes(x=Sample, y=Gene)) + labs(y = gene) + # geom_bar(stat="identity") + geom_boxplot(fill='#A4A4A4') + scale_y_continuous(position = "right", expand = c(0,0)) + coord_flip() + ylim2(p_group) + theme( panel.background = element_rect(fill='transparent'), plot.background = element_rect(fill='transparent', color=NA), axis.text.y=element_blank(), axis.title.y=element_blank() ) return(p) Merge all plots together a large plot

Usage

combind_plots(
  track_plot,
  annot_plot,
  expr_plot,
  track_width,
  legend.position = "bottom",
  t = -20,
  b = 20
)

Arguments

track_plot

plot object of genome tracks

annot_plot

annotation bar for expression

expr_plot

gene expression barplot

track_width

width of tracks

legend.position

legend position, by default will be bottom

t

for alignment of expression barplot, distance to top

b

for alignment of expression barplot, distance to bottom

Value

plot object of combined plot

Examples

NA
#> [1] NA