sp_pcoa: Generating pcoa plot

In Tong-Chen/YSX: For Yishengxin Training

Description

Generating pcoa plot

Usage

sp_pcoa(
  data,
  grp_file,
  shape = "c_t_c_t0304",
  shape_order = NULL,
  color = "",
  color_order = NULL,
  color_v = NULL,
  title = "",
  size = "ct___",
  label = FALSE,
  label_font_size = NULL,
  debug = FALSE,
  file = "data",
  ...
)

Arguments

data	Data file With header line, the first column is the rowname, tab seperated. Each row represents variable (normally genes), each column represents samples.
grp_file	Sample group file with first column as sample names, other columns as sample attributes. Below, color, size, shape variable should be existed in this file. If not supplied, each sample will be treated as one group. And a variable named 'group' can be used to set as color or shape variable.
shape	The variable for point shape.
shape_order	The order for shape variable. Default alphabetical order, accept a string like "'K562','hESC','GM12878','HUVEC','NHEK','IMR90','HMEC'".
color	The variable for group information. Necessary, this variable will be used as group information and color variable as also.
color_order	The order for color variable. Default alphabetical order, accept a string like "'K562','hESC','GM12878','HUVEC','NHEK','IMR90','HMEC'".
color_v	Manually specified colors. Default system default. Accept string in format like '"green", "red"' (both types of quotes needed).
title	Title of picture.
size	The variable for point size. Optional, such as a number or a variable like count, normally should be number column.
label	Label points. Default no-label (FALSE), accept TRUE.
label_font_size	Label font size. Default system default. Accept numbers less than 5 to shrink fonts.
...

Value

A ggplot2 object

Examples

## Not run:
pcoa_data = "pcoa.data"
group_pcoa_data = "group_pcoa.data"
sp_pcoa(data=pcoa_data,grp_file = group_pcoa_data, color = "genotype")
## End(Not run)

Tong-Chen/YSX documentation built on Jan. 25, 2021, 2:49 a.m.