| ... | ... |
@@ -29,6 +29,15 @@ |
| 29 | 29 |
#' @importFrom stats aggregate na.omit |
| 30 | 30 |
#' @importFrom utils head read.delim tail |
| 31 | 31 |
#' @export |
| 32 |
+#' @usage |
|
| 33 |
+#' readPathways( |
|
| 34 |
+#' pathwayFile, |
|
| 35 |
+#' header = FALSE, |
|
| 36 |
+#' pathCol = NULL, |
|
| 37 |
+#' geneCol = NULL, |
|
| 38 |
+#' minGene = 1L, |
|
| 39 |
+#' maxGene = Inf |
|
| 40 |
+#' ) |
|
| 32 | 41 |
readPathways <- function(pathwayFile, header = FALSE, |
| 33 | 42 |
pathCol = NULL, geneCol = NULL, minGene = 1L, maxGene = Inf) {
|
| 34 | 43 |
s <- c("gmt", "txt", "xlsx")
|
| ... | ... |
@@ -35,6 +35,20 @@ |
| 35 | 35 |
#' @importFrom forcats fct_reorder |
| 36 | 36 |
#' @importFrom RColorBrewer brewer.pal |
| 37 | 37 |
#' @export |
| 38 |
+#' @usage |
|
| 39 |
+#' plotDotPlot( |
|
| 40 |
+#' df, |
|
| 41 |
+#' xVar, |
|
| 42 |
+#' yVar, |
|
| 43 |
+#' xLab = xVar, |
|
| 44 |
+#' yLab = NULL, |
|
| 45 |
+#' pTitle = NULL, |
|
| 46 |
+#' fillVar = NULL, |
|
| 47 |
+#' fillCol = NULL, |
|
| 48 |
+#' fillLab = fillVar, |
|
| 49 |
+#' sizeVar = NULL, |
|
| 50 |
+#' sizeLab = sizeVar |
|
| 51 |
+#' ) |
|
| 38 | 52 |
plotDotPlot <- function(df, xVar, yVar, |
| 39 | 53 |
xLab = xVar, yLab = NULL, pTitle = NULL, |
| 40 | 54 |
fillVar = NULL, fillCol = NULL, fillLab = fillVar, |
| ... | ... |
@@ -8,7 +8,7 @@ |
| 8 | 8 |
a named list of 1437 vectors |
| 9 | 9 |
} |
| 10 | 10 |
\usage{
|
| 11 |
-pathwaysGMT |
|
| 11 |
+data(pathwaysGMT) |
|
| 12 | 12 |
} |
| 13 | 13 |
\description{
|
| 14 | 14 |
Raw GMT file is available from |
| ... | ... |
@@ -19,6 +19,6 @@ Raw data location |
| 19 | 19 |
system.file("extdata", "Human_Reactome_November_17_2020_symbol.gmt",
|
| 20 | 20 |
package = "fedup") |
| 21 | 21 |
Script to prepare data |
| 22 |
-system.file("data-raw", "pathwaysGMT.R", package ="fedup")
|
|
| 22 |
+system.file("inst", "script", "pathwaysGMT.R", package ="fedup")
|
|
| 23 | 23 |
} |
| 24 | 24 |
\keyword{datasets}
|
| ... | ... |
@@ -3,19 +3,22 @@ |
| 3 | 3 |
\docType{data}
|
| 4 | 4 |
\name{pathwaysTXT}
|
| 5 | 5 |
\alias{pathwaysTXT}
|
| 6 |
-\title{Example list of yeast SAFE terms obtained from a TXT file.}
|
|
| 6 |
+\title{Example list of SAFE terms obtained from a TXT file.}
|
|
| 7 | 7 |
\format{
|
| 8 |
-a named list of 30 vectors |
|
| 8 |
+a named list of 317 vectors |
|
| 9 | 9 |
} |
| 10 | 10 |
\usage{
|
| 11 |
-pathwaysTXT |
|
| 11 |
+data(pathwaysTXT) |
|
| 12 | 12 |
} |
| 13 | 13 |
\description{
|
| 14 |
-Raw data location |
|
| 15 |
-system.file("extdata", "SAFE_terms.txt", package = "fedup")
|
|
| 14 |
+Raw Excel data file (S5) is available from |
|
| 15 |
+\url{https://boonelab.ccbr.utoronto.ca/supplement/costanzo2016/}
|
|
| 16 | 16 |
} |
| 17 | 17 |
\details{
|
| 18 |
+Raw data location |
|
| 19 |
+system.file("extdata", "SAFE_terms.txt", package = "fedup")
|
|
| 20 |
+ |
|
| 18 | 21 |
Script to prepare data |
| 19 |
-system.file("data-raw", "pathwaysTXT.R", package = "fedup")
|
|
| 22 |
+system.file("inst", "script", "pathwaysTXT.R", package = "fedup")
|
|
| 20 | 23 |
} |
| 21 | 24 |
\keyword{datasets}
|
| ... | ... |
@@ -3,19 +3,22 @@ |
| 3 | 3 |
\docType{data}
|
| 4 | 4 |
\name{pathwaysXLSX}
|
| 5 | 5 |
\alias{pathwaysXLSX}
|
| 6 |
-\title{Example list of yeast SAFE terms obtained from a XLSX file.}
|
|
| 6 |
+\title{Example list of SAFE terms obtained from a XLSX file.}
|
|
| 7 | 7 |
\format{
|
| 8 |
-a named list of 30 vectors |
|
| 8 |
+a named list of 317 vectors |
|
| 9 | 9 |
} |
| 10 | 10 |
\usage{
|
| 11 |
-pathwaysXLSX |
|
| 11 |
+data(pathwaysXLSX) |
|
| 12 | 12 |
} |
| 13 | 13 |
\description{
|
| 14 |
-Raw data location |
|
| 15 |
-system.file("extdata", "SAFE_terms.xlsx", package = "fedup")
|
|
| 14 |
+Raw Excel data file (S5) is available from |
|
| 15 |
+\url{https://boonelab.ccbr.utoronto.ca/supplement/costanzo2016/}
|
|
| 16 | 16 |
} |
| 17 | 17 |
\details{
|
| 18 |
+Raw data location |
|
| 19 |
+system.file("extdata", "SAFE_terms.xlsx", package = "fedup")
|
|
| 20 |
+ |
|
| 18 | 21 |
Script to prepare data |
| 19 |
-system.file("data-raw", "pathwaysXLSX.R", package = "fedup")
|
|
| 22 |
+system.file("inst", "script", "pathwaysXLSX.R", package = "fedup")
|
|
| 20 | 23 |
} |
| 21 | 24 |
\keyword{datasets}
|
| ... | ... |
@@ -5,17 +5,17 @@ |
| 5 | 5 |
\title{Visualizes pathway enrichment and depletion using ggplot.}
|
| 6 | 6 |
\usage{
|
| 7 | 7 |
plotDotPlot( |
| 8 |
- df, |
|
| 9 |
- xVar, |
|
| 10 |
- yVar, |
|
| 11 |
- xLab = xVar, |
|
| 12 |
- yLab = NULL, |
|
| 13 |
- pTitle = NULL, |
|
| 14 |
- fillVar = NULL, |
|
| 15 |
- fillCol = NULL, |
|
| 16 |
- fillLab = fillVar, |
|
| 17 |
- sizeVar = NULL, |
|
| 18 |
- sizeLab = sizeVar |
|
| 8 |
+ df, |
|
| 9 |
+ xVar, |
|
| 10 |
+ yVar, |
|
| 11 |
+ xLab = xVar, |
|
| 12 |
+ yLab = NULL, |
|
| 13 |
+ pTitle = NULL, |
|
| 14 |
+ fillVar = NULL, |
|
| 15 |
+ fillCol = NULL, |
|
| 16 |
+ fillLab = fillVar, |
|
| 17 |
+ sizeVar = NULL, |
|
| 18 |
+ sizeLab = sizeVar |
|
| 19 | 19 |
) |
| 20 | 20 |
} |
| 21 | 21 |
\arguments{
|
| ... | ... |
@@ -6,12 +6,12 @@ |
| 6 | 6 |
pathways using EnrichmentMap (EM) in Cytoscape.} |
| 7 | 7 |
\usage{
|
| 8 | 8 |
plotFemap( |
| 9 |
- gmtFile, |
|
| 10 |
- resultsFile, |
|
| 11 |
- pvalue = 1, |
|
| 12 |
- qvalue = 1, |
|
| 13 |
- netName = "generic", |
|
| 14 |
- netFile = "png" |
|
| 9 |
+ gmtFile, |
|
| 10 |
+ resultsFile, |
|
| 11 |
+ pvalue = 1, |
|
| 12 |
+ qvalue = 1, |
|
| 13 |
+ netName = "generic", |
|
| 14 |
+ netFile = "png" |
|
| 15 | 15 |
) |
| 16 | 16 |
} |
| 17 | 17 |
\arguments{
|
| ... | ... |
@@ -32,8 +32,8 @@ will not be included in the EM (value between 0 and 1; default 1).} |
| 32 | 32 |
jpeg image formats.} |
| 33 | 33 |
} |
| 34 | 34 |
\value{
|
| 35 |
-file name of image to which the network is exported. Also side |
|
| 36 |
- effect of plotting the EM in an open session of Cytoscape. |
|
| 35 |
+file name of image to which the network is exported and an open |
|
| 36 |
+session of Cytoscape (side effect of plotting EM). |
|
| 37 | 37 |
} |
| 38 | 38 |
\description{
|
| 39 | 39 |
Draws a network representation of overlaps among enriched and depleted |
| ... | ... |
@@ -6,12 +6,12 @@ |
| 6 | 6 |
Currently supports the following file format: gmt, txt, xlsx.} |
| 7 | 7 |
\usage{
|
| 8 | 8 |
readPathways( |
| 9 |
- pathwayFile, |
|
| 10 |
- header = FALSE, |
|
| 11 |
- pathCol = NULL, |
|
| 12 |
- geneCol = NULL, |
|
| 13 |
- minGene = 1L, |
|
| 14 |
- maxGene = Inf |
|
| 9 |
+ pathwayFile, |
|
| 10 |
+ header = FALSE, |
|
| 11 |
+ pathCol = NULL, |
|
| 12 |
+ geneCol = NULL, |
|
| 13 |
+ minGene = 1L, |
|
| 14 |
+ maxGene = Inf |
|
| 15 | 15 |
) |
| 16 | 16 |
} |
| 17 | 17 |
\arguments{
|
| ... | ... |
@@ -8,10 +8,10 @@ |
| 8 | 8 |
a character vector with 190 elements (gene IDs) |
| 9 | 9 |
} |
| 10 | 10 |
\usage{
|
| 11 |
-testGene |
|
| 11 |
+data(testGene) |
|
| 12 | 12 |
} |
| 13 | 13 |
\description{
|
| 14 | 14 |
Script to prepare data |
| 15 |
-system.file("data-raw", "genes.R", package = "fedup")
|
|
| 15 |
+system.file("inst", "script", "genes.R", package = "fedup")
|
|
| 16 | 16 |
} |
| 17 | 17 |
\keyword{datasets}
|
