Plots the temporal trend of one or more individual proteins: the measured values (one point per sample), the mean +/- SEM at each timepoint, and the trajectory fitted by analyze.timecourse.
plot.timecourse.protein(
DEprot.timecourse.object,
protein.id,
values = "counts",
reference.time = NULL,
color = "black",
group.colors = NULL,
show.points = TRUE,
show.fit = TRUE,
shape.column = NULL,
log.x = FALSE,
show.stats = TRUE,
panel.border = TRUE,
ncol = NULL,
line.size = 0.8,
point.size = 2,
scale.expression = NULL
)An object of class DEprot.timecourse.
String (or vector of strings) indicating the proteins to plot. The identifiers must correspond to the full row.names of the counts table.
String indicating the quantity displayed on the y-axis. One among: 'counts' (the log2 values as they are), 'log2FC' (log2 fold change relative to reference.time; the counts being already in log2, this is a simple subtraction), 'zscore' (Z-score of the measured values, the fitted curve being centered/scaled with the same mean and SD so that curve and points remain comparable). Aliases are accepted ('fc', 'foldchange', 'log2', 'z', ...). Default: "counts".
Numeric value indicating the timepoint used as baseline when values is 'log2FC'. Default: NULL (the earliest timepoint).
String indicating the color of the line and of the points. Used only when no group.column was defined in the analyses; with several groups use group.colors instead. Default: "black".
Named vector of colors to use for the groups. Default: NULL (automatic).
Logic value indicating whether the individual samples should be displayed. Default: TRUE.
Logic value indicating whether the fitted trajectory should be displayed. Default: TRUE.
String indicating a column from the metadata table to use as factor for the shape of the points (e.g., 'replicate'). The column name is used as title of the shape legend. Default: NULL.
Logic value indicating whether the x-axis should use a log10(time + 1) scale, useful with log-spaced timepoints. Default: FALSE.
Logic value indicating whether padj, amplitude, shape, cluster and rank should be added as subtitle (single protein only). Default: TRUE.
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 when several proteins are plotted. Default: NULL (automatic).
Numeric value indicating the thickness of the fitted line. Default: 0.8.
Numeric value indicating the size of the mean points. Default: 2.
Deprecated, kept for backward compatibility: TRUE is equivalent to values = "zscore", FALSE to values = "counts". Default: NULL.
A plot of class ggplot2, facetted by protein when several proteins are provided.