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Expression Profiles of Genes and Their Isoforms Across Groups

Source: R/profile.R
profiles.Rd

profile_data() summarises the expression of selected genes and of each of their isoforms per sample group (mean and standard deviation), and attaches the differential expression calls. plot_tx_expr() draws the result: one panel per gene, one line per feature (the gene plus its isoforms), coloured by transcript type and faded when not differentially expressed. The table-based prepare_profile_data() produces the same table from loose tables.

Usage

profile_data(self, gene_name, group, levels = NULL, assay = "abundance", ...)

plot_tx_expr(
  self,
  gene_name = NULL,
  group = NULL,
  levels = NULL,
  assay = "abundance",
  log_scale = TRUE,
  label = TRUE,
  ncol = NULL,
  color_palette = NULL,
  ...
)

Arguments

self

An IsoformicExperiment, or (for plot_tx_expr()) a profile table produced by profile_data()/prepare_profile_data().

gene_name

Character vector of gene names or IDs to profile.

group

Name of the col_data column defining the groups (x axis).

levels

Optional order of the group levels. Defaults to the factor levels or the order of appearance.

assay

Name of the transcript assay to summarise (default "abundance").

...

Passed on to methods.

log_scale

Logical, show log2(mean + 1) on the y axis.

label

Logical, label features at the last group level.

ncol

Number of facet columns, NULL for automatic.

color_palette

Named colour vector per transcript type; defaults to the object's palette or tx_type_palette().

Value

profile_data() returns a tibble with columns feature_id, feature_name, feature_type, gene_id, gene_name, group, mean_expr, sd_expr, n_samples and is_de; the grouping variable name is stored in the "group_var" attribute. plot_tx_expr() returns a ggplot object.

Examples

iso <- example_isoformic()
head(profile_data(iso, gene_name = "RBPJ", group = "condition"))
#> # A tibble: 6 × 10
#>   feature_id feature_name feature_type gene_id gene_name group mean_expr sd_expr
#>   <chr>      <chr>        <chr>        <chr>   <chr>     <fct>     <dbl>   <dbl>
#> 1 ENSG00000… RBPJ         gene         ENSG00… RBPJ      pree…   1297.    427.  
#> 2 ENSG00000… RBPJ         gene         ENSG00… RBPJ      cont…   1367.    195.  
#> 3 ENST00000… RBPJ-201     protein_cod… ENSG00… RBPJ      pree…     11.2    25.1 
#> 4 ENST00000… RBPJ-201     protein_cod… ENSG00… RBPJ      cont…      3.95    8.30
#> 5 ENST00000… RBPJ-202     protein_cod… ENSG00… RBPJ      pree…    838.    303.  
#> 6 ENST00000… RBPJ-202     protein_cod… ENSG00… RBPJ      cont…   1095.    169.  
#> # ℹ 2 more variables: n_samples <int>, is_de <chr>
plot_tx_expr(iso, gene_name = c("RBPJ", "EGFR"), group = "condition")