plot_volcano | R Documentation |
Plots a volcano plot with ggplot2
plot_volcano( data_, color = "regulated", p.value.cutoff = 0.05, pos.log2fc.cutoff = 0, neg.log2fc.cutoff = 0, highlight.variables = NULL, highlight.color = NULL, x.axis.title = "log2 fold-change", y.axis.title = "-log10(p-value)", text.size = 6, text.color = "black", point.size = 2, point.alpha = 0.8, highlight.point.size = 3, highlight.point.alpha = 0.8, x.axis.breaks = 1, y.axis.breaks = 1, axis.line.size = 0.5, axis.color = "black", axis.ticks.size = 0.3, axis.title.size = 8, axis.text.size = 6, aspect.ratio = 0.8, use.plotly, view = T, input = "data_t.test", output = "plot_t.test" )
data_ |
data_ |
color |
column for color of points |
p.value.cutoff |
p-value limit for coloring |
pos.log2fc.cutoff |
positive log2 fold-change limit for coloring |
neg.log2fc.cutoff |
negative log2 fold-change limit for coloring |
highlight.variables |
variables to highlight by point.size |
highlight.color |
color to use to highlight proteins |
x.axis.title |
title of x-axis |
y.axis.title |
title of y-axis |
text.size |
size of text in points (5-8) |
text.color |
color of text |
point.size |
point size (0.5-2) |
point.alpha |
transparency (0-1) |
highlight.point.size |
size of point of highlighted variables |
highlight.point.alpha |
transparency of points to be highlighted |
x.axis.breaks |
break size between ticks of x-axis |
y.axis.breaks |
break size between ticks of y-axis |
axis.line.size |
width of axes lines |
axis.color |
color of axes lines |
axis.ticks.size |
width of axis ticks |
axis.title.size |
size of axis title |
axis.text.size |
size of axis labels |
aspect.ratio |
y/x ratio |
use.plotly |
make interactive plots with ggplotly() (default: T if html document) |
view |
view plot |
input |
name of input data |
output |
name of output data |
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