Description Usage Arguments Value Note Author(s) See Also
Creates a 3-paneled plot of a selected gene: panel 1 = genomic position vs. raw coverage data, panel 2 = genomic position vs. moderated t statistic from linear model at that position, panel 3 = genomic position vs. predicted state for that position, with annotated exons overlaid.
1 2 3 4 5 | plotGene(getRegionObject, ind = NULL, genename = NULL, tstats, pos,
annotation, counts, group, bppad = 50, axpad = 50, prettyskips = T,
skiplines = T, countsheader = F, countssep = "\t", tabname = NULL,
plotfile = NULL, width = 900, height = 750, plottitle = NULL,
chromosome, legendloc = "bottomleft", scalefac = 0.5, ylim = c(0, 9))
|
getRegionObject |
The name of an object created with
|
ind |
index in the provided |
genename |
name of the gene (as listed in the
provided |
tstats |
Vector of t-statistics that was used to
create |
pos |
vector of genomic positions corresponding to
|
annotation |
data frame containing exon annotation
to use (see |
counts |
Raw coverage data used to obtain
|
group |
a vector containing the group labels for the columns of counts. Only 2 groups are permitted at this time. These labels are used in the plot's legend, so generally they are character strings (rather than, say, 0/1). |
bppad |
the number of bases to plot outside of the designated region (default 50). Essentially, use this to "zoom" in (decrease bppad) or out (increase bppad) on the plotted region. |
axpad |
how much wider (in bases) you'd like the x-axis to be, compared to the plotted area |
prettyskips |
If TRUE, plot
counts/states/t-statistics contiguously, even if there
are zero entries between them (i.e., even though pos may
not indicate that contiguous postions are being plotted).
Note that in general, when plotting just one exon, this
is not an issue as exons tend to contain contiguous data.
So, |
skiplines |
if TRUE, add a light vertical line to the plot indicating an eliminated "low-coverage" nucleotide |
countsheader |
If TRUE, the |
countssep |
If reading counts from a text file, the separator used in that file. |
tabname |
If counts is a database file, the name of
the table that was dumped into that database. (See
|
plotfile |
Optional string containing a file you'd like to put the plot into (if NULL, plot appears interactively). Should have a .jpg extension. |
width |
Only used when |
height |
Only used when |
plottitle |
Optional main title to use on your plot. Defaults to chromosome: start-end (referring to plotted REGION) |
chromosome |
The chromosome corresponding to the
exon being plotted, in the same format as chromosomes are
listed in the supplied |
legendloc |
Can be one of "topright","bottomright","topleft",or "bottomleft" indicating where the legend (indicating group label on raw count plot) should be located. Defaults to "bottomleft." |
scalefac |
How should we offset counts (so that we can log-transform everything, even zero counts)? Defaults to 0.5, derfinder uses an offset of 32. |
ylim |
Equivalent to ylim argument in plot: what should the lower and upper limits be on the y-axis of the top panel of plot be? Defaults to c(0,9). |
Plots (either on screen or in the supplied .jpg file) the
following: top panel = genomic position vs. raw coverage
data, middle panel = genomic position vs. moderated t
statistic from linear model at that position, bottom panel
= genomic position vs. predicted state for that position,
with annotated exons overlaid. States are as follows: gray
= not expressed, black = equally expressed, red =
overexpressed (in whatever group = 1 represented in
getRegions
), green = underexpressed.
Provide exactly one of ind
and genename
.
Recommendation is to provide geneName
.
Alyssa Frazee
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