Description Usage Arguments Value
View source: R/equal_sample.R View source: R/FlowSOM_tSNE_Output.R
自动生成系列tSNE图;
自动生成系列tSNE图;
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 | 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"
)
|
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 |
none
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