ScatterView: Scatter plot

In WubingZhang/MAGeCKFlute: Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens

Scatter plot

Description

Scatter plot supporting groups.

Usage

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",
  ...
)

Arguments

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 or numeric, specifying how many standard deviation will be used as cutoff.
auto_cut_x	Boolean or numeric, specifying how many standard deviation will be used as cutoff on x-axis.
auto_cut_y	Boolean or numeric, specifying how many standard deviation will be used as cutoff on y-axis
auto_cut_diag	Boolean or numeric, specifying how many standard deviation will be used 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'.

Value

An object created by ggplot, which can be assigned and further customized.

Author(s)

Wubing Zhang

Examples

file3 = file.path(system.file("extdata", package = "MAGeCKFlute"),
"testdata/mle.gene_summary.txt")
dd = ReadBeta(file3)
ScatterView(dd, x = "Pmel1_Ctrl", y = "Pmel1", label = "Gene",
auto_cut = 1, groups = "topright", top = 5, display_cut = TRUE)
ScatterView(dd, x = "Pmel1_Ctrl", y = "Pmel1", label = "Gene",
auto_cut = 2, model = "ninesquare", top = 5, display_cut = TRUE)

WubingZhang/MAGeCKFlute documentation built on Jan. 27, 2024, 2:43 p.m.