draw_density_plots: draw_density_plots

In XinleiChen001/cytofexplorer: A data analysis package for cytof users

Description

自动生成每个marker的直方图（密度图）；

自动生成每个marker的直方图（密度图）；

Usage

draw_density_plots(
  combined_data_plot,
  groups,
  all_markers,
  cluster_color = dif_seq_rainbow,
  cluster_name = "metacluster",
  output_dir = "cluster_density_plots",
  major_cond = "Tissue_Type",
  cluster_id = NULL,
  xlim = NULL,
  free_x = F,
  trans_method = "simpleAsinh"
)

draw_density_plots(
  combined_data_plot,
  groups,
  all_markers,
  cluster_color = dif_seq_rainbow,
  cluster_name = "metacluster",
  output_dir = "cluster_density_plots",
  major_cond = "Tissue_Type",
  cluster_id = NULL,
  xlim = NULL,
  free_x = F,
  trans_method = "simpleAsinh"
)

Arguments

combined_data_plot	数据框或者矩阵，附带有(meta)cluster、降维结果(t_sne_1,t_sne_2)的表达矩阵
groups	实验组的Metadata信息,其中必需包含列名：”Short_name“
cluster_color	tSNE图的亚群的配色方案，默认dif_seq_rainbow
cluster_name	用过分析的cluster名称
output_dir	输出数据文件夹名称
major_cond	选择groups中一个列名做为展现差异的major_cond
cluster_id	指定显示的cluster
xlim	指定x轴范围，例如：c(0,5)，只在free_x=F的时候有效
free_x	True或者FALSE，设置是否每张图X-轴取值范围是否自动，建议设置为F
trans_method	数据转化方式，有四种："CytofAsinh"，"simpleAsinh"；"0_to_Max"，所有Marker的信号强度除以最大值，线性转换，通过除以各通道信号的最大值把数值scale到0~1；"Min_to_Max"，线性转换，最小值转换成0，最大值转换成1，最大限度展现population的表达差异

Value

none

XinleiChen001/cytofexplorer documentation built on Oct. 31, 2020, 5:59 p.m.