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Plot feature abundance over time

Source: R/plot_trend.R
plot_trend.Rd

Plot trend of feature abundances / expression over time by mean and standard deviation (SD) for each group. Accepts either a SummarizedExperiment object (computing mean/SD internally via calc_mean_sd()) or a pre-computed table from calc_mean_sd().

Usage

plot_trend(
  se_obj,
  assay = 1,
  groups = NULL,
  features,
  title = "Feature",
  ylab = "Abundance",
  errorbar = TRUE,
  fontsize = 8
)

Arguments

se_obj

A SummarizedExperiment object, or a data.frame from calc_mean_sd() with columns: Feature, Time, Group, Mean, SD.

assay

Assay index when se_obj is a SummarizedExperiment (default: 1 = original, 2 = time-0 normalised).

groups

Groups to be plotted, if NULL, all groups will be used (default is NULL)

features

Features to be plotted, if NULL, an error will be raised

title

Title of the plot (default is "Feature")

ylab

Y axis label of the plot (default is "Abundance")

errorbar

Whether to plot error bars (default is TRUE)

fontsize

Font size for the plot (default is 8)

Value

Plot of feature abundances over time by mean and SD

Examples

data(example_obj)
plot_trend(example_obj,
    features = sample(rownames(example_obj), 4))
#> Group not specified. Plotting all groups: IFNbeta, IFNgamma, LPS, untreated