Skip to contents

Plot expression as a lollipop chart

get_expression_lollipop.Rd

Displays selected genes as stem-and-dot (lollipop) plots. By default, expression is summarized per group (mean across replicates). With by = "sample", the plot shows individual samples.

Usage

get_expression_lollipop(
  x,
  genes,
  sample_group = NULL,
  group_column = NULL,
  by = c("group", "sample"),
  sample_order = c("input", "group", "expression"),
  facet_by = c("auto", "gene", "none"),
  log_transform = TRUE,
  facet_scale = "free_y",
  point_size = 6,
  line_size = 1.2,
  label = TRUE,
  label_digits = 1,
  display_id = NULL,
  display_from = NULL,
  display_orgdb = NULL
)

Arguments

x

A VISTA object.

genes

Character vector (<=15 genes) to plot.

sample_group

Optional character vector of groups (from group_column) to include.

group_column

Optional column name in sample_info to use for grouping samples.

by

One of "group" (default; summarize replicates by group) or "sample" (show individual samples).

sample_order

Ordering used when by = "sample": "input" preserves the current sample order, "group" groups samples by group_column, and "expression" ranks samples by mean expression across the selected genes.

facet_by

Faceting mode: "auto" (default; facet by gene when more than one gene is requested), "gene", or "none". For multiple genes, "none" falls back to "gene" to avoid unreadable combined panels.

log_transform

Logical; log2-transform expression before plotting.

facet_scale

Scaling option passed to facet_wrap() when plotting multiple genes.

point_size

Numeric size of the dots.

line_size

Numeric size of the stems.

label

Logical; draw numeric labels above the dots.

label_digits

Integer; digits to show in labels when label = TRUE.

display_id

Optional ID/column name to use for labels/facets. If supplied and present in rowData(x), those values are used; otherwise falls back to ID mapping.

display_from

Optional source ID type for mapping (used when display_id is not found in rowData).

display_orgdb

Optional OrgDb object used for ID mapping when display_id is set but not found in rowData.

Value

An object returned by this function.

A ggplot2 object.

Examples

v <- example_vista()
genes <- head(rownames(v), 5)
p <- get_expression_lollipop(v, genes = genes)
print(p)

data("count_data", package = "VISTA")
data("sample_metadata", package = "VISTA")

vista <- create_vista(
  counts = count_data[1:200, ],
  sample_info = sample_metadata[1:6, ],
  column_geneid = "gene_id",
  group_column = "cond_long",
  group_numerator = "treatment1",
  group_denominator = "control"
)
#> estimating size factors
#> estimating dispersions
#> gene-wise dispersion estimates
#> mean-dispersion relationship
#> final dispersion estimates
#> fitting model and testing

genes <- rownames(vista)[1:3]
get_expression_lollipop(vista, genes = genes)

get_expression_lollipop(vista, genes = genes[1:2], by = "sample")