xVolcano | R Documentation |
xVolcano
is supposed to draw a volcano plot
xVolcano(data, column.lfc = "lfc", column.fdr = "fdr", cutoff.lfc = 1, cutoff.fdr = 0.05, colors = c("#EEEEEE", "darkgrey", "pink", "red"), column.label = NULL, top = 10, top.direction = c("both", "up", "down"), label.size = 2, label.color = "black", label.alpha = 0.8, label.padding = 0.5, label.arrow = 0.01, label.force = 0.5, xlim = NULL, ylim = NULL, y.scale = c("normal", "log"), xlab = expression(log[2]("fold change")), ylab = expression(-log[10]("FDR")), font.family = "sans", signature = TRUE)
data |
a data frame |
column.lfc |
a character specifying 'lfc' column (log2-transformed fold change) |
column.fdr |
a character specifying 'fdr' column |
cutoff.lfc |
a numeric defining 'lfc' cutoff. By default, it is 1 (at least 2-fold changes) |
cutoff.fdr |
a numeric defining 'fdr' cutoff. By default, it is 0.05 |
colors |
a 4-element vector for color-coded points. By default, it is c("#EEEEEE","darkgrey","pink","red") |
column.label |
a character specifying 'label' column |
top |
an integer specifying the number of the top points for labellings |
top.direction |
the direction (up- and down-regulated) of the top points. It can be one of 'both' (up- and down-regulated), 'up' (up-regulated only) and 'down' (down-regulated only) |
label.size |
the label size |
label.color |
the label color |
label.alpha |
the 0-1 value specifying transparency of labelling |
label.padding |
the padding around the labeled |
label.arrow |
the arrow pointing to the labeled |
label.force |
the repelling force between overlapping labels |
xlim |
the limits in the x-axis |
ylim |
the limits in the y-axis |
y.scale |
how to transform the y scale. It can be "normal" for no transformation, and "log" for log-based transformation |
xlab |
the x labelling. By default, it is expression(log[2]("fold change")) |
ylab |
the y labelling. By default, it is expression(-log[10]("FDR")) |
font.family |
the font family for texts |
signature |
logical to indicate whether the signature is assigned to the plot caption. By default, it sets TRUE |
a ggplot object
none
xVolcano
## Not run: # Load the library library(XGR) RData.location <- "http://galahad.well.ox.ac.uk/bigdata/" ## End(Not run)