sp_manhattan2_plot: Generating manhattan plot

In Tong-Chen/ImageGP: For ImageGP cloud platform (https://www.bic.ac.cn/BIC)

Generating manhattan plot

Description

Generating manhattan plot

Usage

sp_manhattan2_plot(
  data,
  ID_var = "ID",
  FDR_var = "FDR",
  grp_var = "Phylum",
  sig_col = "level",
  status_col_level = c(),
  pvalue = 0.05,
  shape_col = NULL,
  color_var = NULL,
  alpha = 0.4,
  grp_var_order = c(),
  color_var_order = c(),
  shape_col_order = c(),
  log10_transform_fdr = TRUE,
  filename = NULL,
  point_label_var = "CTctctCT",
  title = "",
  x_label = NULL,
  y_label = "Negative log10 FDR",
  legend.position = "right",
  point_size = "ct___",
  ...
)

Arguments

data	Data frame or data file (with header line, the first column will not be treated as the rowname, tab seperated).
ID_var	Name of ID column.
FDR_var	Name of FDR column.
grp_var	Group variable for ordering points.
sig_col	Significant column.Optional, in sample data significant.
status_col_level	Changing the order of status column values. Normally, the unique values of status column would be sorted alphabetically.
pvalue	Set the filter threshold for defining significance. Default "0.05".
shape_col	Column for points shapes.
color_var	Column for color points. Default the same as group variable.
alpha	Transparent alpha value.Default 0.4, Accept a float from 0(transparent), 1(opaque).
grp_var_order	Group variable order, like "'Rhizobiales', 'Actinomycetales'".
color_var_order	Color variable order. Default same as grp_var.
shape_col_order	Levels for shapes, like "'Sig','nonSig'".
log10_transform_fdr	Get -log10(FDR) for column given to FDR_var. Default FALSE, accept TRUE.
filename	Output picture to given file.
point_label_var	Name of columns containing labels for points.
title	Title of picture.
x_label	Xlab label.Default NULL.
y_label	Ylab label.Default "Negative log10 FDR".
legend.position	Position of legend, accept top, bottom, left, right, none or c(0.8,0.8).
...

Value

A ggplot2 object

Examples

## Not run:
manhattan_data = "manhattan.data"

sp_manhattan2_plot(data=manhattan_data, ID_var='ID', FDR_var='FDR', title="test1", point_size=2, point_label_var = "Labels")
## End(Not run)

Tong-Chen/ImageGP documentation built on April 14, 2025, 12:54 p.m.