dm_plotProportions: Plot feature proportions

Description Usage Arguments Value

View source: R/dm_plotProportions.R

Description

Plot observed and/or estimated feature proportions.

Usage

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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.