plotGeneralQC: plotGeneralQC
In IMB-Computational-Genomics-Lab/ascend: ascend - Analysis of Single Cell Expression, Normalisation, and Differential expression
Description
Usage
Arguments
Details
Value
Examples
Description
This function generates a series of plots that can be used to assess the
present quality of an EMSet.
Usage
1
plotGeneralQC(object)
Arguments
object
An EMSet object.
Details
The plots are as follows:
Library Size per Cell: A series of barplots depicting the
library size of each cell in descending order.
Library Size: A histogram depicting the distribution of
library sizes across the dataset.
Average Gene Count: A histogram depicting number of cells vs
mean gene expression.
Average Gene Count (Log2): A histogram depicting number of
cells vs Log2 mean gene expression.
Average Gene Count (Log10): A histogram depicting number of
cells vs Log2 mean gene expression.
Log 10 Average Gene Count (Smooth Scatter): Smooth scatter
plot of number of cells vs Log10 mean gene expression.
Top Genes Per Sample: Violin/beehive plots depicting
proportion of top genes to total cell expression per sample.
Top Gene Expression: Boxplots depicting top 25 genes in terms
of expression.
If controls are defined, two additional plots are generated:
Percentage Control Expression: Histograms depicting number of
cells with the contribution of control genes as a percentage of total counts.
Proportion of Control Expression: Violin/beehive plots for
each sample and control, depicting the proportion of controls to total
expression.
Value
A list of plot objects.
Examples
1
2
3
4
5
# Load EMSet
EMSet <- ascend::raw_set
# Plot general QC
general_qc_plots <- plotGeneralQC(EMSet)
IMB-Computational-Genomics-Lab/ascend documentation built on Aug. 29, 2019, 4:10 a.m.
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Description Usage Arguments Details Value Examples
Description
This function generates a series of plots that can be used to assess the present quality of an EMSet.
Usage
1 | plotGeneralQC(object)
|
Arguments
object |
An |
Details
The plots are as follows:
Library Size per Cell: A series of barplots depicting the library size of each cell in descending order.
Library Size: A histogram depicting the distribution of library sizes across the dataset.
Average Gene Count: A histogram depicting number of cells vs mean gene expression.
Average Gene Count (Log2): A histogram depicting number of cells vs Log2 mean gene expression.
Average Gene Count (Log10): A histogram depicting number of cells vs Log2 mean gene expression.
Log 10 Average Gene Count (Smooth Scatter): Smooth scatter plot of number of cells vs Log10 mean gene expression.
Top Genes Per Sample: Violin/beehive plots depicting proportion of top genes to total cell expression per sample.
Top Gene Expression: Boxplots depicting top 25 genes in terms of expression.
If controls are defined, two additional plots are generated:
Percentage Control Expression: Histograms depicting number of cells with the contribution of control genes as a percentage of total counts.
Proportion of Control Expression: Violin/beehive plots for each sample and control, depicting the proportion of controls to total expression.
Value
A list of plot objects.
Examples
1 2 3 4 5 | # Load EMSet
EMSet <- ascend::raw_set
# Plot general QC
general_qc_plots <- plotGeneralQC(EMSet)
|
R Package Documentation
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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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