Chapter 12 Plot genes of interest

Sometimes it is useful to view boxplots of the expression of a gene for all individual samples. This function allows genes of interest to be plotted in detail.

Multiple names can be provided. The names of the genes are

groups_for_DE <- seq_data$Tissue_Region %>% unique()

DE4Rumi::plot_genes_of_interest(norm_exp_data = vst_norm_data,
           DE_full_out = DE_out,
           se_data = seq_data,
           gene_annotations = gene_annot,
           selected_genes = c("AGRP", "IGF1"),
           top_level_colname = Tissue_Region,
           sample_colname = sample_names,
           results_contrast_factor = Treatment,
           top_level_groups = groups_for_DE,
           plot_groups_colname = Treatment,
           max_genes_per_plot = 3,
           x_label = "Treatment",
           p_thresh = 0.05)

## Joining, by = "sample_names"

## Joining, by = "Treatment"
## Joining, by = "Treatment"

## Joining, by = c("gene_name", "top_level")
## Joining, by = c("gene_name", "top_level")

## $`1`