plotUnsupervisedMarkers: plotUnsupervisedMarkers
In jasonserviss/CIMseq: CIMseq is a software suite for analysis of scRNAseq data that has been produced using the cellular interactions by multiplet sequencing method
Description
Usage
Arguments
Value
Author(s)
Examples
Description
Plot method for spUnsupervised objects to highlight "markers", typically
genes thought to be discreetly expressed in one cell type, in the context of
the dimensionality reduction and classification results.
Usage
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plotUnsupervisedMarkers(singlets, multiplets, ...)
## S4 method for signature 'CIMseqSinglets,CIMseqMultiplets'
plotUnsupervisedMarkers(singlets,
multiplets, markers = NULL, log = TRUE, normalize = TRUE,
pal = col40(), ...)
Arguments
singlets
CIMseqSinglets; A CIMseqSinglets object.
multiplets
CIMseqMultiplets; A CIMseqMultiplets object.
...
additional arguments to pass on.
markers
character; A vector with markers to be included plot.
log
logical; Use log2 values? See plotCountsData.
normalize
logical; Use [0, 1] normalized values?
See processMarkers.
pal
character; A palette of colors with length(pal) = length(markers).
Value
A ggplot2 object with plot. See examples or the plotting vignette
for further help.
Author(s)
Jason T. Serviss
Examples
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2
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4
#Plot
p <- plotUnsupervisedMarkers(
CIMseqSinglets_test, CIMseqMultiplets_test, markers = "CD74"
)
jasonserviss/CIMseq documentation built on Jan. 11, 2020, 4:42 a.m.
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Description Usage Arguments Value Author(s) Examples
Description
Plot method for spUnsupervised objects to highlight "markers", typically genes thought to be discreetly expressed in one cell type, in the context of the dimensionality reduction and classification results.
Usage
1 2 3 4 5 6 7 | plotUnsupervisedMarkers(singlets, multiplets, ...)
## S4 method for signature 'CIMseqSinglets,CIMseqMultiplets'
plotUnsupervisedMarkers(singlets,
multiplets, markers = NULL, log = TRUE, normalize = TRUE,
pal = col40(), ...)
|
Arguments
singlets |
CIMseqSinglets; A CIMseqSinglets object. |
multiplets |
CIMseqMultiplets; A CIMseqMultiplets object. |
... |
additional arguments to pass on. |
markers |
character; A vector with markers to be included plot. |
log |
logical; Use log2 values? See |
normalize |
logical; Use [0, 1] normalized values?
See |
pal |
character; A palette of colors with length(pal) = length(markers). |
Value
A ggplot2 object with plot. See examples or the plotting vignette for further help.
Author(s)
Jason T. Serviss
Examples
1 2 3 4 | #Plot
p <- plotUnsupervisedMarkers(
CIMseqSinglets_test, CIMseqMultiplets_test, markers = "CD74"
)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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