This function do a CCI plot
Usage
plot_cci(
graph,
colors,
plt_name,
coords,
emax = NULL,
leg = FALSE,
low = 25,
high = 75,
ignore_alpha = FALSE,
log = FALSE,
efactor = 8,
vfactor = 12,
vnames = T,
pg = NULL,
vnamescol = NULL
)Arguments
- graph
Paths of single condition LR data
- colors
Cell type (Cluster) Colors
- plt_name
Plot Name (Title)
- coords
object coordinates
- emax
Max MeanLR across the all inputs, if its not defined, the method going to consider the max find within a sample
- leg
Set color legend
- low
Lower threshold: This parameter low and high defines the edges
- high
Higher threshould which will be filtered. Edges within the interval [low\,high] are filtered.
- ignore_alpha
not include transparency on the plot
- log
logscale the interactions
- efactor
edge scale factor
- vfactor
edge scale factor
- vnames
remove vertex labels
- pg
pagerank values
Examples
paths <- c(
"CTR" = system.file("extdata",
"CTR_LR.csv",
package = "CrossTalkeR"
),
"EXP" = system.file("extdata",
"EXP_LR.csv",
package = "CrossTalkeR"
)
)
genes <- c("TGFB1")
output <- system.file("extdata", package = "CrossTalkeR")
data <- generate_report(paths,
genes,
out_path = paste0(output, "/"),
threshold = 0,
out_file = "vignettes_example.html",
output_fmt = "html_document",
report = FALSE
)
#> Warning: file("") only supports open = "w+" and open = "w+b": using the former
#> Error in read.table(file = file, header = header, sep = sep, quote = quote, dec = dec, fill = fill, comment.char = comment.char, ...): no lines available in input
plot_cci(
graph = data@graphs$CTR,
colors = data@colors,
plt_name = "Example 1",
coords = data@coords[igraph::V(data@graphs$CTR)$name, ],
emax = NULL,
leg = FALSE,
low = 0,
high = 0,
ignore_alpha = FALSE,
log = FALSE,
efactor = 8,
vfactor = 12,
vnames = TRUE
)
#> Error in data@graphs: no applicable method for `@` applied to an object of class "function"