Skip to content
This repository has been archived by the owner on Jan 24, 2024. It is now read-only.

Update modeling.R #203

Open
wants to merge 4 commits into
base: master
Choose a base branch
from
Open

Update modeling.R #203

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
0a6579e
Update modeling.R
stemangiola May 20, 2021
1902dec
Update analysis.R
stemangiola May 20, 2021
90611d7
Update analysis.R
stemangiola May 20, 2021
f7761e5
Update modeling.R
stemangiola May 20, 2021
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
8 changes: 4 additions & 4 deletions R/analysis.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -49,7 +49,7 @@ netAnalysis_contribution <- function(object, signaling, signaling.name = NULL, w
pairLR <- pairLR[pairLR.name.use,]
}

prob <- prob[,,pairLR.name.use]
prob <- prob[,,pairLR.name.use, drop=FALSE]
Copy link
Owner

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This is not necessary as we have if (length(dim(prob)) == 2) below.


if (length(dim(prob)) == 2) {
prob <- replicate(1, prob, simplify="array")
Expand Down Expand Up @@ -981,7 +981,7 @@ rankNet <- function(object, slot.name = "netP", mode = c("comparison", "single")
}
}
idx.t <- setdiff(1:nrow(prob), sources.use)
prob[idx.t, , ] <- 0
prob[idx.t, , ,drop=FALSE] <- 0
}
if (!is.null(targets.use)) {
if (is.character(targets.use)) {
Expand All @@ -992,7 +992,7 @@ rankNet <- function(object, slot.name = "netP", mode = c("comparison", "single")
}
}
idx.t <- setdiff(1:nrow(prob), targets.use)
prob[ ,idx.t, ] <- 0
prob[ ,idx.t, ,drop=FALSE] <- 0
}
if (sum(prob) == 0) {
stop("No inferred communications for the input!")
Expand Down Expand Up @@ -1058,7 +1058,7 @@ rankNet <- function(object, slot.name = "netP", mode = c("comparison", "single")
}
}
idx.t <- setdiff(1:nrow(prob), targets.use)
prob[ ,idx.t, ] <- 0
prob[ ,idx.t, , drop=FALSE] <- 0
}
if (sum(prob) == 0) {
stop("No inferred communications for the input!")
Expand Down
4 changes: 2 additions & 2 deletions R/modeling.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -375,10 +375,10 @@ computeCommunProbPathway <- function(object = NULL, net = NULL, pairLR.use = NUL
group <- factor(pairLR.use$pathway_name, levels = pathways)
prob.pathways <- aperm(apply(prob, c(1, 2), by, group, sum), c(2, 3, 1))
pathways.sig <- pathways[apply(prob.pathways, 3, sum) != 0]
prob.pathways.sig <- prob.pathways[,,pathways.sig]
prob.pathways.sig <- prob.pathways[,,pathways.sig, drop=FALSE]
idx <- sort(apply(prob.pathways.sig, 3, sum), decreasing=TRUE, index.return = TRUE)$ix
pathways.sig <- pathways.sig[idx]
prob.pathways.sig <- prob.pathways.sig[, , idx]
prob.pathways.sig <- prob.pathways.sig[, , idx, drop=FALSE]

if (is.null(object)) {
netP = list(pathways = pathways.sig, prob = prob.pathways.sig)
Expand Down