genepattern.HeatMapImage: From a GCT file, create a HeatMap Image, using the jar from...

In drmjc/metaGSEA: Meta-analysis of GSEA analyses, including intra- and inter-experiment comparisons

Description

You can either connect to GenePattern server, and submit HeatMapImage jobs to the server, or directly execute the jar file locally,

Usage

genepattern.HeatMapImage(in.file, out.file = NULL, method = c("local",
  "server"), gp.connection = NULL, format = "png", row.size = 16,
  column.size = 16, show.grid = "yes", grid.color = "0:0:0",
  show.row.descriptions = "yes", show.row.names = "yes",
  rows.to.highlight = "", row.highlight.color = "255:0:0",
  color.scheme = "row normalized", color.palette = "",
  use.color.gradient = "no", memory = "-Xmx512m", verbose = FALSE,
  overwrite = FALSE)

Arguments

in.file	a single gct/res or odf file.
out.file	if NULL, the outfile will be in the same dir as in.file, with the extenstion changed dependant on format
method	“local” or “server”
gp.connection	if method="server" then you should specify a connection to the server. see examples.
format	picture format, one of: “png”, “tiff”, “jpeg”, “eps”, “bmp”. “png” is default & recommended. “tiff” look good for publication.
row.size	see HeatMapImage help at Broad's GenePattern server.
column.size	see HeatMapImage help at Broad's GenePattern server.
show.grid	see HeatMapImage help at Broad's GenePattern server.
grid.color	see HeatMapImage help at Broad's GenePattern server.
show.row.descriptions	see HeatMapImage help at Broad's GenePattern server.
show.row.names	see HeatMapImage help at Broad's GenePattern server.
rows.to.highlight	see HeatMapImage help at Broad's GenePattern server.
row.highlight.color	see HeatMapImage help at Broad's GenePattern server.
color.scheme	see HeatMapImage help at Broad's GenePattern server.
color.palette	see HeatMapImage help at Broad's GenePattern server.
use.color.gradient	see HeatMapImage help at Broad's GenePattern server.
memory	see HeatMapImage help at Broad's GenePattern server.
verbose	logical: verbose messages?
overwrite	overwrite existing images?

Details

Shout out to Joshua Gould, Broad Institute who wrote the jar in the first place.

Value

none. creates heatmaps.

Author(s)

Mark Cowley, 2009-08-19

Examples

# not run
## 1) running locally:
# genepattern.HeatMapImage(in.file=<myfile.gct>, method="local", format="png")
## 2)
# library(GenePattern)
# gp.con <- gp.login("http://pwbc.garvan.unsw.edu.au/gp", "<username>", "<password>")
# genepattern.HeatMapImage(in.file=<myfile.gct>, method="server", gp.connection=gp.con, format="png")

drmjc/metaGSEA documentation built on Aug. 8, 2020, 1:53 p.m.