Description Usage Arguments Value Author(s) Examples
Scatter plot supporting groups.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 | ScatterView(
data,
x = "x",
y = "y",
label = 0,
model = c("none", "ninesquare", "volcano", "rank")[1],
x_cut = NULL,
y_cut = NULL,
slope = 1,
intercept = NULL,
auto_cut = FALSE,
auto_cut_x = auto_cut,
auto_cut_y = auto_cut,
auto_cut_diag = auto_cut,
groups = NULL,
group_col = NULL,
groupnames = NULL,
label.top = TRUE,
top = 0,
toplabels = NULL,
display_cut = FALSE,
color = NULL,
shape = 16,
size = 1,
alpha = 0.6,
main = NULL,
xlab = x,
ylab = y,
legend.position = "none",
...
)
|
data |
Data frame. |
x |
A character, specifying the x-axis. |
y |
A character, specifying the y-axis. |
label |
An integer or a character specifying the column used as the label, default value is 0 (row names). |
model |
One of "none" (default), "ninesquare", "volcano", and "rank". |
x_cut |
An one or two-length numeric vector, specifying the cutoff used for x-axis. |
y_cut |
An one or two-length numeric vector, specifying the cutoff used for y-axis. |
slope |
A numberic value indicating slope of the diagonal cutoff. |
intercept |
A numberic value indicating intercept of the diagonal cutoff. |
auto_cut |
Boolean, take 1.5 fold standard deviation as cutoff. |
auto_cut_x |
Boolean, take 1.5 fold standard deviation as cutoff on x-axis. |
auto_cut_y |
Boolean, take 1.5 fold standard deviation as cutoff on y-axis. |
auto_cut_diag |
Boolean, take 1.5 fold standard deviation as cutoff on diagonal. |
groups |
A character vector specifying groups. Optional groups include "top", "mid", "bottom", "left", "center", "right", "topleft", "topcenter", "topright", "midleft", "midcenter", "midright", "bottomleft", "bottomcenter", "bottomright". |
group_col |
A vector of colors for specified groups. |
groupnames |
A vector of group names to show on the legend. |
label.top |
Boolean, specifying whether label top hits. |
top |
Integer, specifying the number of top terms in the groups to be labeled. |
toplabels |
Character vector, specifying terms to be labeled. |
display_cut |
Boolean, indicating whether display the dashed line of cutoffs. |
color |
A character, specifying the column name of color in the data frame. |
shape |
A character, specifying the column name of shape in the data frame. |
size |
A character, specifying the column name of size in the data frame. |
alpha |
A numeric, specifying the transparency of the dots. |
main |
Title of the figure. |
xlab |
Title of x-axis |
ylab |
Title of y-axis. |
legend.position |
Position of legend, "none", "right", "top", "bottom", or a two-length vector indicating the position. |
... |
Other available parameters in function 'geom_text_repel'. |
An object created by ggplot
, which can be assigned and further customized.
Wubing Zhang
1 2 3 4 5 | file3 = file.path(system.file("extdata", package = "MAGeCKFlute"),
"testdata/mle.gene_summary.txt")
dd = ReadBeta(file3)
ScatterView(dd, x = "dmso", y = "plx", label = "Gene",
x_cut = 1, y_cut = 1, groups = "topright", top = 5, display_cut = TRUE)
|
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