giDensityPlot | R Documentation |

This function plot the genomic instability distribution, gaussian fits and null distribution if available

giDensityPlot(inferCNV, legend = c("topleft", "top", "topright", "none"), ...)

`inferCNV` |
Object of class inferCNV |

`legend` |
Character string indicating the location of the legend. none to not include it |

`...` |
Additional parameters for plot() |

None, a figure is created in the default output device

[giLikelihood()] to estimate the relative likelihood, [genomicInstabilityScore()] to estimate the genomic instability score for each cell in the dataset, and [inferCNV()] to infer the enrichment of loci-blocks in the gene expression data.

eh <- ExperimentHub::ExperimentHub() dset <- eh[["EH5419"]] tpm_matrix <- SummarizedExperiment::assays(dset)$TPM set.seed(1) tpm_matrix <- tpm_matrix[, sample(ncol(tpm_matrix), 500)] cnv <- inferCNV(tpm_matrix) cnv <- genomicInstabilityScore(cnv) cnv <- giLikelihood(cnv, distros=c(3, 3), tumor=2:3) giDensityPlot(cnv)

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.