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### =========================================================================
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### "sgraph" (and related) methods
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### -------------------------------------------------------------------------
setOldClass("igraph")
.EDGE_WEIGHTS <- c(1, 0.2, 0.1, 0.4)
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### .make_igraph_from_sgedges()
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###
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### 'sgedges' must be a data.frame as returned by:
### sgedges( , keep.dup.edges=TRUE)
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### or a DataFrame as returned by:
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### sgedges( , keep.dup.edges=FALSE)
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### Valid extra cols are: "label", "label.color", "lty", "color", "width"
### and "UATXHcount". They are used to set graphical parameters on the edges.
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.precook_igraph_edges_from_sgedges <- function(sgedges)
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{
required_colnames <- c("from", "to", "ex_or_in", "tx_id")
extra_colnames <- c("label", "label.color", "lty", "color",
"width", "UATXHcount")
extract_colnames <- c(required_colnames,
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intersect(extra_colnames, colnames(sgedges)))
ans <- sgedges[ , extract_colnames, drop=FALSE]
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ex_or_in <- ans[ , "ex_or_in"]
ex_or_in_levels <- levels(ex_or_in)
if (!identical(ex_or_in_levels, EX_OR_IN_LEVELS2)
&& !identical(ex_or_in_levels, EX_OR_IN_LEVELS))
stop("\"ex_or_in\" column has invalid levels")
if (!("label.color" %in% extract_colnames))
ans$label.color <- "blue"
if (!("lty" %in% extract_colnames))
ans$lty <- c("solid", "solid", "dashed", "solid")[ex_or_in]
if (!("color" %in% extract_colnames))
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ans$color <- c("orange", "darkgrey", "grey", "black")[ex_or_in]
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if (!("width" %in% extract_colnames)
&& "UATXHcount" %in% extract_colnames) {
min_UATXHcount <- min(ans$UATXHcount)
if (min_UATXHcount < 0L) {
warning("'UATXHcount' column contains negative values. Cannot use ",
"it to set the widths of the edges.")
} else {
max_UATXHcount <- max(ans$UATXHcount)
if (max_UATXHcount <= 0L) {
warning("'UATXHcount' column has no positive values. Cannot use ",
"it to set the widths of the edges.")
} else {
ans$width <- 20.0 * ans$UATXHcount / max(ans$UATXHcount)
}
}
}
ans
}
.make_igraph <- function(d)
{
## Prepare the 'vertices' argument to pass to graph.data.frame().
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nodes <- sgnodes(d)
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color <- c("gray", rep.int("white", length(nodes)-2L), "gray")
label.color <- "black"
vertices <- data.frame(name=nodes, color=color, label.color=label.color)
## Make the igraph object.
g <- graph.data.frame(d, vertices=vertices)
layout.kamada.kawai.deterministic <- function(...)
{
set.seed(33L)
layout.kamada.kawai(...)
}
## Set its layout attribute.
g$layout <- layout.kamada.kawai.deterministic
#g$layout <- layout.sgraph
g
}
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### 'sgedges0' must be a data.frame as returned by:
### sgedges( , keep.dup.edges=TRUE)
.make_igraph_from_sgedges0 <- function(sgedges0, gene_id=NA,
tx_id.as.edge.label=FALSE)
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{
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if (!is.data.frame(sgedges0))
stop("'sgedges0' must be a data.frame")
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if (!isTRUEorFALSE(tx_id.as.edge.label))
stop("'tx_id.as.edge.label' must be TRUE or FALSE")
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d <- .precook_igraph_edges_from_sgedges(sgedges0)
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if (tx_id.as.edge.label)
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d$label <- d$tx_id
.make_igraph(d)
}
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### 'sgedges' must be a DataFrame as returned by:
### sgedges( , keep.dup.edges=FALSE)
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### or by:
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### sgedges2( )
.make_igraph_from_sgedges <- function(sgedges, gene_id=NA,
tx_id.as.edge.label=FALSE)
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{
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if (!is(sgedges, "DataFrame"))
stop("'sgedges' must be a DataFrame")
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if (!isTRUEorFALSE(tx_id.as.edge.label))
stop("'tx_id.as.edge.label' must be TRUE or FALSE")
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d <- .precook_igraph_edges_from_sgedges(sgedges)
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if (tx_id.as.edge.label)
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d$label <- sapply(d$tx_id, paste, collapse=",")
d$tx_id <- NULL
## Turning 'd' into an ordinary data.frame. (Looks like 'as.data.frame()'
## on a DataFrame ignores the 'stringsAsFactors' arg so we use
## 'data.frame(as.list())' instead.)
d <- data.frame(as.list(d), stringsAsFactors=FALSE)
.make_igraph(d)
}
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### sgraph() extractor
###
### Returns the splicing graph in an Ragraph object.
###
setGeneric("sgraph", signature="x",
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function(x, gene_id=NA, keep.dup.edges=FALSE,
tx_id.as.edge.label=FALSE, as.igraph=FALSE)
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standardGeneric("sgraph")
)
setMethod("sgraph", "ANY",
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function(x, gene_id=NA, keep.dup.edges=FALSE,
tx_id.as.edge.label=FALSE, as.igraph=FALSE)
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{
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sgedges <- sgedges(x, gene_id=gene_id, keep.dup.edges=keep.dup.edges)
sgraph(sgedges, tx_id.as.edge.label=tx_id.as.edge.label,
as.igraph=as.igraph)
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}
)
setMethod("sgraph", "data.frame",
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function(x, gene_id=NA, keep.dup.edges=FALSE,
tx_id.as.edge.label=FALSE, as.igraph=FALSE)
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{
if (!identical(gene_id, NA))
stop("the 'gene_id' arg is not supported ",
"when 'x' is a data.frame")
if (!identical(keep.dup.edges, FALSE))
stop("the 'keep.dup.edges' arg is not supported ",
"when 'x' is a data.frame")
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igraph <- .make_igraph_from_sgedges0(x,
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tx_id.as.edge.label=tx_id.as.edge.label)
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sgraph(igraph, as.igraph=as.igraph)
}
)
setMethod("sgraph", "DataFrame",
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function(x, gene_id=NA, keep.dup.edges=FALSE,
tx_id.as.edge.label=FALSE, as.igraph=FALSE)
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{
if (!identical(gene_id, NA))
stop("the 'gene_id' arg is not supported ",
"when 'x' is a DataFrame")
if (!identical(keep.dup.edges, FALSE))
stop("the 'keep.dup.edges' arg is not supported ",
"when 'x' is a DataFrame")
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igraph <- .make_igraph_from_sgedges(x,
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tx_id.as.edge.label=tx_id.as.edge.label)
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sgraph(igraph, as.igraph=as.igraph)
}
)
setMethod("sgraph", "igraph",
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function(x, gene_id=NA, keep.dup.edges=FALSE,
tx_id.as.edge.label=FALSE, as.igraph=FALSE)
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{
if (!identical(gene_id, NA))
stop("the 'gene_id' arg is not supported ",
"when 'x' is an igraph object")
if (!identical(keep.dup.edges, FALSE))
stop("the 'keep.dup.edges' arg is not supported ",
"when 'x' is an igraph object")
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if (!identical(tx_id.as.edge.label, FALSE))
stop("the 'tx_id.as.edge.label' arg is not supported ",
"when 'x' is an igraph object")
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if (!isTRUEorFALSE(as.igraph))
stop("'as.igraph' must be TRUE or FALSE")
if (as.igraph) {
## Need to load the igraph package so the user can display, plot,
## and manipulate the returned object.
library(igraph)
return(x) # no-op
}
make_Ragraph_from_igraph(x)
}
)
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### sgraph2() extractor
###
### Same as sgraph() except that uninformative nodes (i.e. SSids) are removed.
###
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sgraph2 <- function(x, gene_id=NA, tx_id.as.edge.label=FALSE, as.igraph=FALSE)
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{
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sgraph(sgedges2(x, gene_id=gene_id),
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tx_id.as.edge.label=tx_id.as.edge.label, as.igraph=as.igraph)
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}
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### "plot" method.
###
setMethod("plot", c("SplicingGraphs", "ANY"),
function(x, y, gene_id=NA)
{
if (missing(gene_id)) {
if (missing(y)) {
gene_id <- NA
} else {
gene_id <- y
}
} else {
if (!missing(y))
warning("'y' is ignored when plotting a SplicingGraphs ",
"object and 'gene_id' is supplied")
}
if (!isSingleStringOrNA(gene_id))
stop("the supplied gene id must be a single string (or NA)")
x_names <- names(x)
if (!is.null(x_names) && is.na(gene_id))
stop("You need to specify a gene id when 'x' has names ",
"e.g. 'plot(sg, \"some gene id\")'. Get all valid ",
"gene ids with 'unique(names(sg))'.")
plot(sgraph(x, gene_id=gene_id))
}
)
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### slideshow()
###
slideshow <- function(x)
{
if (!is(x, "SplicingGraphs"))
stop("'x' must be a SplicingGraphs object")
for (gene_id in unique(names(x))) {
ntx <- sum(names(x) == gene_id)
cat("Plotting gene ", gene_id, " (", ntx, " transcripts). ", sep="")
plot(x, gene_id)
cat("Press <Enter> for next...")
readLines(n=1)
}
}
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