From: Shana White <vandersm@mail.uc.edu>
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGlincs@130008 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -34,8 +34,9 @@ |
34 | 34 |
#' |
35 | 35 |
|
36 | 36 |
edge_mapping_info <- |
37 |
-function(expanded_edges, data_added = FALSE, significance_markup = FALSE){ |
|
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- expanded_edges <- expanded_edges[,-c(1)] |
|
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+function(expanded_edges, data_added = FALSE, significance_markup = FALSE, |
|
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+ tidy_edge = TRUE){ |
|
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+ #expanded_edges <- expanded_edges[,-c(1)] |
|
39 | 40 |
for(i in 1:nrow(expanded_edges)){ |
40 | 41 |
if (expanded_edges$subtype1[i] == "activation"){ |
41 | 42 |
expanded_edges$color[i] = "#b20000" |
... | ... |
@@ -145,6 +146,27 @@ function(expanded_edges, data_added = FALSE, significance_markup = FALSE){ |
145 | 146 |
} |
146 | 147 |
} |
147 | 148 |
} |
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- expanded_edges <- expanded_edges[,c(3:4, 1:2, 5:ncol(expanded_edges))] |
|
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+ #edge_map <- edge_map[,c(2,5,3,1,4:ncol(edge_map))] |
|
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+ expanded_edges<- cbind(expanded_edges[,c("entry1", "entry2","edgeID", |
|
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+ "entry1accession", "entry2accession")], |
|
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+ expanded_edges[,c(6:ncol(expanded_edges))]) |
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+ expanded_edges <- expanded_edges[order(expanded_edges$edgeID),] |
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+ |
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+ if (tidy_edge == TRUE) { |
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+ edge_IDs <- seq(min(expanded_edges$edgeID), max(expanded_edges$edgeID)) |
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+ for (i in edge_IDs){ |
|
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+ if(data_added == TRUE){ |
|
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+ expanded_edges <- tidy_edge(edges = expanded_edges, |
|
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+ edge_id = edge_IDs[i], |
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+ data_added = TRUE, |
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+ by_significance = TRUE) |
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+ } |
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+ if(data_added == FALSE){ |
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+ expanded_edges <- tidy_edge(edges = expanded_edges, |
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+ edge_id = edge_IDs[i], |
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+ data_added = FALSE) |
|
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+ } |
|
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+ } |
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+ } |
|
149 | 171 |
return(expanded_edges) |
150 | 172 |
} |
151 | 173 |
new file mode 100644 |
... | ... |
@@ -0,0 +1,96 @@ |
1 |
+#' Tidy up pathway by combining edges inside of edge_mapping_info |
|
2 |
+#' @description Combine edges that share nodes and have other commonalities |
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3 |
+#' @export |
|
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+#' @param edges The edge dataframe |
|
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+#' @param edge_id The numeric value for the edge_id |
|
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+#' @param by_significance A logical indicator; option if data is added |
|
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+#' @param by_number A logical indicator; gives rough estimate of edge amount |
|
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+#' @return A data frame that has had the given edge condensed for viewing |
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+#' @examples \dontrun{ |
|
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+#' if (tidy_edge == TRUE) { |
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+#' edge_IDs <- seq(min(expanded_edges$edgeID), max(expanded_edges$edgeID)) |
|
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+#' for (i in edge_IDs){ |
|
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+#' if(data_added == TRUE){ |
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+#' expanded_edges <- tidy_edge(edges = expanded_edges, |
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+#' edge_id = edge_IDs[i], |
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+#' data_added = TRUE, |
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+#' by_significance = TRUE) |
|
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+#' } |
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+#' if(data_added == FALSE){ |
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+#' expanded_edges <- tidy_edge(edges = expanded_edges, |
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+#' edge_id = edge_IDs[i], |
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+#' data_added = FALSE) |
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+#' } |
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+#' } |
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+#' |
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+#'} |
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+#'} |
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+ |
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+tidy_edge <- function(edges, edge_id, data_added = TRUE, |
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+ by_significance = FALSE, by_number = TRUE){ |
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+ edge <- edges[edges$edgeID == edge_id,] |
|
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+ edges_1 <- edges[edges$edgeID != edge_id,] |
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+ if (!data_added){ |
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+ entry1accessions <- paste(unique(edge$entry1accession), collapse =",") |
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+ entry2accessions <- paste(unique(edge$entry2accession), collapse =",") |
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+ entry1symbols <- paste(unique(edge$entry1symbol), collapse = ",") |
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+ entry2symbols <- paste(unique(edge$entry2symbol), collapse = ",") |
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+ tooltip <- paste(entry1symbols, edge$value[1], entry2symbols) |
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+ edge$entry1symbol[1] <- entry1symbols |
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+ edge$entry2symbol[1] <- entry2symbols |
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+ edge$entry1accession[1] <- entry1accessions |
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+ edge$entry2accession[1] <- entry2accessions |
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+ edge$tooltip[1] <- tooltip |
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+ reduced_edge <- edge[1,] |
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+ } |
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+ if (data_added){ |
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+ if (sum(edge$has_data) == 0){ |
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+ entry1accessions <- paste(unique(edge$entry1accession), collapse =",") |
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+ entry2accessions <- paste(unique(edge$entry2accession), collapse =",") |
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+ entry1symbols <- paste(unique(edge$entry1symbol), collapse = ",") |
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+ entry2symbols <- paste(unique(edge$entry2symbol), collapse = ",") |
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+ tooltip <- paste(entry1symbols, edge$value[1], entry2symbols) |
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+ edge$entry1symbol[1] <- entry1symbols |
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+ edge$entry2symbol[1] <- entry2symbols |
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+ edge$entry1accession[1] <- entry1accessions |
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+ edge$entry2accession[1] <- entry2accessions |
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+ edge$tooltip[1] <- tooltip |
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+ reduced_edge <- edge[1,] |
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+ } |
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+ |
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+ if (sum(edge$has_data) != 0 ){ |
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+ reduced_edge <- edge[edge$has_data != 0,] |
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+ if(by_significance == TRUE){ |
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+ for (i in 1:length(unique(reduced_edge$color))){ |
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+ rp <- reduced_edge[reduced_edge$color == unique(reduced_edge$color)[i],] |
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+ reduced_edge <- reduced_edge[reduced_edge$color != unique(reduced_edge$color)[i],] |
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+ entry1accessions <- paste(unique(rp$entry1accession), collapse =",") |
|
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+ entry2accessions <- paste(unique(rp$entry2accession), collapse =",") |
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+ entry1symbols <- paste(unique(rp$entry1symbol), collapse = ",") |
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+ entry2symbols <- paste(unique(rp$entry2symbol), collapse = ",") |
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+ tooltip <- paste(unique(rp$tooltip), collapse = " , ") |
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+ average_summary_score <- mean(rp$summary_score) |
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+ rp$entry1symbol[1] <- entry1symbols |
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+ rp$entry2symbol[1] <- entry2symbols |
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+ rp$entry1accession[1] <- entry1accessions |
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+ rp$entry2accession[1] <- entry2accessions |
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+ rp$tooltip[1] <- tooltip |
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+ rp$summary_score[1] <- average_summary_score |
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+ |
|
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+ if(by_number == TRUE) { |
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+ col <- rp$color[1] |
|
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+ thresh <- min(5, (nrow(rp)-1)) |
|
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+ value <- 1-(0.1*thresh) |
|
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+ col1 <- round(value*(col2rgb(col)[1])) |
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+ col2 <- round(value*(col2rgb(col)[2])) |
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+ col3 <- round(value*(col2rgb(col)[3])) |
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+ rp$color[1] <- rgb(col1, col2, col3, maxColorValue = 255) |
|
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+ } |
|
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+ reduced_edge <- rbind(rp[1,], reduced_edge) |
|
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+ } |
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+ } |
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+ } |
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+ } |
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+ edges <- rbind (edges_1, reduced_edge) |
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+ return(edges) |
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+} |
|
0 | 97 |
\ No newline at end of file |
... | ... |
@@ -5,7 +5,7 @@ |
5 | 5 |
\title{Prepare edges for mapping} |
6 | 6 |
\usage{ |
7 | 7 |
edge_mapping_info(expanded_edges, data_added = FALSE, |
8 |
- significance_markup = FALSE) |
|
8 |
+ significance_markup = FALSE, tidy_edge = TRUE) |
|
9 | 9 |
} |
10 | 10 |
\arguments{ |
11 | 11 |
\item{expanded_edges}{The data frame object generated via the function |
12 | 12 |
new file mode 100644 |
... | ... |
@@ -0,0 +1,45 @@ |
1 |
+% Generated by roxygen2: do not edit by hand |
|
2 |
+% Please edit documentation in R/tidy_edge.R |
|
3 |
+\name{tidy_edge} |
|
4 |
+\alias{tidy_edge} |
|
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+\title{Tidy up pathway by combining edges inside of edge_mapping_info} |
|
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+\usage{ |
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7 |
+tidy_edge(edges, edge_id, data_added = TRUE, by_significance = FALSE, |
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+ by_number = TRUE) |
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+} |
|
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+\arguments{ |
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+\item{edges}{The edge dataframe} |
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+ |
|
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+\item{edge_id}{The numeric value for the edge_id} |
|
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+ |
|
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+\item{by_significance}{A logical indicator; option if data is added} |
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+ |
|
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+\item{by_number}{A logical indicator; gives rough estimate of edge amount} |
|
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+} |
|
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+\value{ |
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+A data frame that has had the given edge condensed for viewing |
|
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+} |
|
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+\description{ |
|
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+Combine edges that share nodes and have other commonalities |
|
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+} |
|
25 |
+\examples{ |
|
26 |
+\dontrun{ |
|
27 |
+if (tidy_edge == TRUE) { |
|
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+ edge_IDs <- seq(min(expanded_edges$edgeID), max(expanded_edges$edgeID)) |
|
29 |
+ for (i in edge_IDs){ |
|
30 |
+ if(data_added == TRUE){ |
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31 |
+ expanded_edges <- tidy_edge(edges = expanded_edges, |
|
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+ edge_id = edge_IDs[i], |
|
33 |
+ data_added = TRUE, |
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+ by_significance = TRUE) |
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+ } |
|
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+ if(data_added == FALSE){ |
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+ expanded_edges <- tidy_edge(edges = expanded_edges, |
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+ edge_id = edge_IDs[i], |
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+ data_added = FALSE) |
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+ } |
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+ } |
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+ |
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+} |
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+} |
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+} |