Plots the fitted trajectories of the trending proteins, one panel per cluster. The lines are colored by cluster membership (c-means) and the cluster centroid (trend line) is overlaid. With values = "zscore" this reproduces the classical Mfuzz-like representation.
plot.timecourse.profiles(
DEprot.timecourse.object,
clusters = NULL,
top.n = NULL,
values = "zscore",
reference.time = NULL,
free.y = NULL,
line.color = NULL,
membership.palette = c("#3B4CC0", "#7B9FF9", "#EDD1C2", "#E36C55", "#B40426"),
centroid.color = "black",
centroid.size = 1,
line.alpha = 0.4,
log.x = FALSE,
panel.border = TRUE,
ncol = NULL
)An object of class DEprot.timecourse.
Numeric value (or vector) indicating the cluster(s) to plot. Default: NULL (all the clusters).
Numeric value indicating how many best-ranked proteins of each cluster should be displayed. Default: NULL (all the proteins).
String indicating the quantity displayed on the y-axis. One among: 'zscore' (Z-score of each fitted trajectory: shape only, and the scale on which the clustering was actually performed), 'log2FC' (log2 fold change of the fitted curve relative to reference.time, which preserves the real amplitude of the response), 'counts' (the fitted log2 values as they are: absolute abundances, hence the clusters will overlap vertically). Aliases are accepted ('fc', 'foldchange', 'log2', 'z', ...). Default: "zscore".
Numeric value indicating the timepoint used as baseline when values is 'log2FC'. Default: NULL (the earliest timepoint).
Logic value indicating whether each facet should have its own y-axis. Default: NULL, meaning TRUE when values is 'counts' and FALSE otherwise.
String indicating a single color for the individual protein lines. When provided, it replaces the membership gradient. Default: NULL (the lines are colored by membership).
Vector of colors used for the membership gradient, ignored when line.color is provided. Default: c("#3B4CC0", "#7B9FF9", "#EDD1C2", "#E36C55", "#B40426").
String indicating the color of the trend line, that is, of the cluster centroid. Default: "black".
Numeric value indicating the thickness of the trend line. Default: 1.
Numeric value indicating the transparency of the individual protein lines. Default: 0.4.
Logic value indicating whether the x-axis should use a log10(time + 1) scale. Default: FALSE.
Logic value indicating whether a border should be drawn around each panel. Default: TRUE.
Numeric value indicating the number of columns of the facet grid. Default: NULL (automatic).
A plot of class ggplot2.