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check_gene()
- check if a gene is valid
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combind_plots()
- 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
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genome_track_map()
- Function to make the genome track map with combined expression and group information
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make_peak_group()
- separate peaks based on their CRE-gene linkages on diferent groups
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plot_annotation_bar()
- Function to plot annotation bar for each sample
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plot_expr_barplot()
- Barplot of gene expression level
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plot_genome_track()
- functions to plot out the genome track
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plot_giggle()
- Plot motif or tf binding information
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query_exprssion()
- Get expression of each sample
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query_linkage()
- query linkage of a gene or a genome region
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query_meta()
- query metadata of samples
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tf_binding()
- Obtain TF binding information of genome region(s)