plot_de_confidence(x, gene_name)shows, for the isoforms of the given genes, the median log2 fold-change over the Salmon replicates with its 95% interval, coloured by the confidence class ofde_confidence()and with the shape marking the calls of the primary differential expression test. An interval that crosses zero, a faded colour or an ambiguous isoform tell the reader not to trust the call.plot_isoform_correlation(x, gene_name)draws the correlation between the replicates of every pair of isoforms of a gene. Strongly negative cells (outlined when ambiguous) mark isoforms whose reads cannot be told apart.plot_inf_rv(x)shows the distribution of the inferential relative variance per transcript type with the cutoff used to call isoforms uncertain.confidence_palette()gives the colours of the confidence classes.
Usage
confidence_palette()
plot_de_confidence(self, gene_name, ncol = 1L, ...)
plot_isoform_correlation(self, gene_name, ncol = 1L, ...)
plot_inf_rv(self, top_types = 6L, ...)Arguments
- self
An IsoformicExperiment with uncertainty tables (see
add_uncertainty()).- gene_name
Gene names or IDs to plot.
- ncol
Number of panel columns.
- ...
Unused.
- top_types
Number of the most frequent transcript types to show.