GC_sequence {geneviewer} | R Documentation |
Update Sequence Display of a GC Chart Cluster
Description
Modify the sequence display and break markers of specified clusters within a GC chart.
Usage
GC_sequence(
GC_chart,
show = TRUE,
cluster = NULL,
y = 50,
sequenceStyle = list(),
markerStyle = list(),
...
)
Arguments
GC_chart |
A GC chart object. |
show |
Logical, whether to display the sequence (default is TRUE). |
cluster |
Numeric or character vector specifying clusters to update. |
y |
Vertical position of the sequence line (default is 50). |
sequenceStyle |
A list of styling options for the sequence line. |
markerStyle |
A list of styling options for the sequence break markers. |
... |
Additional customization arguments for sequence display. |
Details
This function allows customization of the sequence line and break markers in a GC chart. It offers options to adjust the sequence line ('sequenceStyle') and break markers ('markerStyle'). The 'y' parameter can be used to set the vertical position of the sequence.
Value
An updated GC chart with modified sequence display settings.
Examples
genes_data <- data.frame(
start = c(10, 90, 130, 170, 210),
end = c(40, 120, 160, 200, 240),
name = c('Gene 1', 'Gene 3', 'Gene 4', 'Gene 5', 'Gene 6'),
group = c('A', 'B', 'B', 'A', 'C'),
cluster = c(1, 1, 2, 2, 2)
)
# Basic usage
GC_chart(genes_data, cluster ="cluster", group = "group", height = "200px") %>%
GC_labels("name") %>%
GC_sequence(show = TRUE, y = 50, cluster = NULL)
# Customize sequence and marker styles
GC_chart(genes_data, cluster="cluster", group = "group", height = "200px") %>%
GC_scale(hidden = TRUE, scale_breaks = TRUE) %>%
GC_sequence(
start = NULL,
end = NULL,
sequenceStyle = list(
stroke = "blue",
strokeWidth = 1
# Any other CSS style
),
markerStyle = list(
stroke = "blue",
strokeWidth = 1,
gap = 3,
tiltAmount = 5
# Any other CSS style
)
) %>%
GC_legend(FALSE)