DEG.plot.static {ORFik} | R Documentation |
Plot setup:
X-axis: mean counts
Y-axis: Log2 fold changes
For explanation of plot, see DEG.analysis
DEG.plot.static( dt, output.dir = NULL, p.value = 0.05, plot.title = "", plot.ext = ".pdf", width = 6, height = 6, dot.size = 0.4, xlim = "auto", ylim = "bidir.max", relative.name = paste0("DEG_plot", plot.ext) )
dt |
a data.table with the results from |
output.dir |
a character path, default NULL(no save), or a directory to save to a file. Relative name of file, specified by 'relative.name' argument. |
p.value |
a numeric, default 0.05 in interval (0,1) or "" to not show. What p-value used for the analysis? Will be shown as a caption. |
plot.title |
title for plots, usually name of experiment etc |
plot.ext |
character, default: ".pdf". Alternatives: ".png" or ".jpg". |
width |
numeric, default 6 (in inches) |
height |
numeric, default 6 (in inches) |
dot.size |
numeric, default 0.4, size of point dots in plot. |
xlim |
numeric vector or character preset, default: "bidir.max" (Equal in both + / - direction, using max value + 0.5 of meanCounts column in dt). If you want ggplot to decide limit, set to "auto". For numeric vector, specify min and max x limit: like c(-5, 5) |
ylim |
numeric vector or character preset, default: "bidir.max" (Equal in both + / - direction, using max value + 0.5 of LFC column in dt). If you want ggplot to decide limit, set to "auto". For numeric vector, specify min and max y limit: like c(-10, 10) |
relative.name |
character, Default: |
a ggplot object
Other DifferentialExpression:
DTEG.analysis()
,
DTEG.plot()
,
te.table()
,
te_rna.plot()
df <- ORFik.template.experiment() df.rna <- df[df$libtype == "RNA",] #dt <- DEG.analysis(df.rna) #Default scaling #DEG.plot.static(dt) #Manual scaling #DEG.plot.static(dt, xlim = c(-2, 2), ylim = c(-2, 2))