dm_plotProportions: Plot feature proportions

In gosianow/DRIMSeq: Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq

Description

Plot observed and/or estimated feature proportions.

Usage

dm_plotProportions(counts, group, md = NULL, fit_full = NULL, main = NULL,
  plot_type = "boxplot1", order_features = TRUE, order_samples = TRUE,
  group_colors = NULL, feature_colors = NULL)

Arguments

counts	Matrix with rows corresponding to features and columns corresponding to samples. Row names are used as labels on the plot.
group	Factor that groups samples into conditions.
md	Data frame with additional sample information.
fit_full	Matrix of estimated proportions with rows corresponding to features and columns corresponding to samples. If NULL, nothing is plotted.
main	Character vector with main title for the plot. If NULL, nothing is plotted.
plot_type	Character defining the type of the plot produced. Possible values "barplot", "boxplot1", "boxplot2", "lineplot", "ribbonplot".
order_features	Logical. Whether to plot the features ordered by their expression.
order_samples	Logical. Whether to plot the samples ordered by the group variable. If FALSE order from the sample(x) is kept.
group_colors	Character vector with colors for each group.
feature_colors	Character vector with colors for each feature.

Value

ggplot object with the observed and/or estimated with Dirichlet-multinomial model feature ratios. Estimated proportions are marked with diamond shapes.

gosianow/DRIMSeq documentation built on Aug. 8, 2020, 10:29 a.m.