Description Usage Arguments Details Value Author(s) References See Also Examples
Given 3 or more mass spec experiments as msarc
objects,
this function draws a heat map of the similarity among the experiments.
Similarity may be calculated based on similarity of scores, or simply by
the presence or absence of individual UniProt accession id's.
1 | msarc.plotHeatmap(msalist, method = "euclidean", useScore = T, ...)
|
msalist |
a list of |
method |
Correlation method to pass to |
useScore |
If true (the default), use the score of each peptide in computing the correlation. If false, just use the presence or absence of each protein in each experiment. |
... |
Other parameters to pass to |
The samples must have distinct filenames, or this function will
fail. You can load the samples from mass spec files, or just explicitly
set object$filename for each msarc
object. These filenames will also
be used as labels in the heat map.
the distance matrix calculated by dist
.
Gord Brown
Gregory R. Warnes. Includes R source code and/or documentation contributed by: Ben Bolker, Lodewijk Bonebakker, Robert Gentleman, Wolfgang Huber Andy Liaw, Thomas Lumley, Martin Maechler, Arni Magnusson, Steffen Moeller, Marc Schwartz and Bill Venables (2011). gplots: Various R programming tools for plotting data. R package version 2.10.1. http://CRAN.R-project.org/package=gplots
See also heatmap.2
from package gplots
and
dist
from package stats
.
1 2 | data('sample_cluster',package="msarc")
## Not run: msarc.plotHeatmap(sample_cluster)
|
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