draw_tsne_figs: draw_tsne_figs

Description Usage Arguments Value

View source: R/equal_sample.R View source: R/FlowSOM_tSNE_Output.R

Description

自动生成系列tSNE图;

自动生成系列tSNE图;

Usage

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draw_tsne_figs(
  combined_data_plot,
  groups,
  cluster_color = dif_seq_rainbow,
  cluster_name = "metacluster",
  output_dir = "cluster_tsne_plots",
  major_cond = "Tissue_Type",
  reduction_dm1 = "tsne_1",
  reduction_dm2 = "tsne_2",
  dot_size = 4,
  text_size = 30,
  show_contour = FALSE,
  contour_line_size = 0.5,
  contour_bins = 25,
  contour_colour = "grey",
  group_seq = NULL,
  output_format = "pdf"
)

draw_tsne_figs(
  combined_data_plot,
  groups,
  cluster_color = dif_seq_rainbow,
  cluster_name = "metacluster",
  output_dir = "cluster_tsne_plots",
  major_cond = "Tissue_Type",
  reduction_dm1 = "tsne_1",
  reduction_dm2 = "tsne_2",
  dot_size = 4,
  text_size = 30,
  show_contour = FALSE,
  contour_line_size = 0.5,
  contour_bins = 25,
  contour_colour = "grey",
  group_seq = NULL,
  output_format = "pdf"
)

Arguments

combined_data_plot

数据框或者矩阵,附带有(meta)cluster聚类、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

选择groups中一个列名做为展现差异的major_cond

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

reduction_dm1

combined_data_plot降维产生的维度,默认"tsne_1"

reduction_dm2

combined_data_plot降维产生的维度,默认"tsne_2"

dot_size

散点图点的大小,默认是4

show_contour

布尔型变量,决定是否显示等高线背景

contour_line_size

设置等高线的宽度,默认0.5

contour_bins

设置等高线的层数,默认25

contour_colour

设置等高线的颜色,默认"grey"

group_seq

设置各组顺序,格式实例: group_seq=c("PBMC","Biopsy"),注:括号内为各组名称;

output_format

输出数据文件格式:"tiff"和“pdf”,默认"pdf"

edge_data

画网络图的时候,存储网络连接数据

cluster_barplot_data

包含cluster通道信息的Vector,用来生成cluster的丰度直方图

cluster_labels_size

控制cluster label的大小,默认30

show_axis

是否显示坐标轴,默认是TRUE

show_cluster_labels

决定是否显示cluster label,TRUE 显示Label,FALSE 不显示

groups_to_show

指定要显示的condition(major_cond中的一个或者多个),如不设置直接统计全部;

edge_line_size

连线的宽度

edge_layer

连线的图层位置,"back"和"front",决定连线图层在散点图的后面或前面

Value

none


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