Skip to contents

Fold-change line plot across comparisons

Source: R/bioccheck_roxygen_fixes.R, R/viz_related.R
get_foldchange_lineplot.Rd

Plots log2 fold-change trajectories for selected genes across multiple comparisons, optionally clustering genes.

Usage

get_foldchange_lineplot(
  x,
  sample_comparisons,
  genes = NULL,
  display_id = NULL,
  display_from = NULL,
  display_orgdb = NULL,
  km = NULL,
  facet_by = c("none", "cluster"),
  facet_scales = "fixed",
  facet_nrow = NULL,
  facet_ncol = NULL,
  alpha = 0.5,
  palette = NULL,
  show_summary = TRUE,
  summary_color = NULL,
  summary_linewidth = 1,
  summary_fun = c("median", "mean"),
  base_size = 14
)

Arguments

x

A VISTA object containing differential expression results.

sample_comparisons

Character vector of comparison names to include.

genes

Optional character vector of gene identifiers to plot. Defaults to all genes.

display_id

Optional ID/column name used to interpret genes and map the returned cluster table to display-friendly labels.

display_from

Optional source ID type for mapping when display_id is not present in rowData(x).

display_orgdb

Optional OrgDb object used for identifier mapping when display_id is not present in rowData(x).

km

Optional integer specifying the number of k-means clusters to compute; NULL disables clustering.

facet_by

Faceting mode: "none" (default) or "cluster" when k-means clustering is requested.

facet_scales

Facet scales argument passed to facet_wrap() when facet_by = "cluster" (default "fixed").

facet_nrow, facet_ncol

Optional layout passed to facet_wrap() when faceting.

alpha

Numeric alpha applied to individual gene lines.

palette

Optional named or unnamed color vector used for cluster lines.

show_summary

Logical; overlay a summary line per cluster when TRUE.

summary_color

Color used for the summary line. When NULL, uses the first comparison color (if stored) for consistency across plots.

summary_linewidth

Numeric line width for the summary line.

summary_fun

Character string selecting "median" or "mean" for the summary statistic.

base_size

Numeric base theme size.

Value

An object returned by this function.

A list with plot (the ggplot2 object) and clustered_data (gene-to-cluster assignments).

Examples

v <- example_vista()
comp <- names(comparisons(v))[1]
genes <- head(as.character(comparisons(v)[[comp]]$gene_id), 5)
p <- get_foldchange_lineplot(v, sample_comparison = comp, genes = genes)
print(p)
#> $plot
#> `geom_line()`: Each group consists of only one observation.
#> ℹ Do you need to adjust the group aesthetic?
#> `geom_line()`: Each group consists of only one observation.
#> ℹ Do you need to adjust the group aesthetic?

#> 
#> $clustered_data
#>                         gene_id    display_gene cluster
#> ENSG00000000003 ENSG00000000003 ENSG00000000003     All
#> ENSG00000000419 ENSG00000000419 ENSG00000000419     All
#> ENSG00000000457 ENSG00000000457 ENSG00000000457     All
#> ENSG00000000460 ENSG00000000460 ENSG00000000460     All
#> ENSG00000000971 ENSG00000000971 ENSG00000000971     All
#>