chord_plot | R Documentation |
Chord plot is used to visualize complex relationships between samples and genes, as well as between pathways and genes.
chord_plot(
data,
multi_colors = "VividColors",
color_seed = 10,
color_alpha = 0.3,
link_visible = TRUE,
link_dir = -1,
link_type = "diffHeight",
sector_scale = "Origin",
width_circle = 3,
dist_name = 3,
label_dir = "Vertical",
dist_label = 0.3,
label_scale = 0.8
)
data |
Dataframe: Shared DEGs of all paired comparisons in all samples expression dataframe of RNA-Seq. (1st-col: Genes, 2nd-col~: Samples). |
multi_colors |
Character: color palette. Default: "VividColors", options: "VividColors", "RainbowColors". |
color_seed |
Numeric: rand seed for VividColors. Default: 10. |
color_alpha |
Numeric: color alpha. Default: 0.50, min: 0.00, max: 1.00. |
link_visible |
Logical: links visible. Default: TRUE, options: TRUE, FALSE. |
link_dir |
Numeric: links direction, use with link_type. Default: -1, options: -1, 0, 1, 2. |
link_type |
Character: links type, use with link_dir. Default: "diffHeight", options: "diffHeight", "arrows". |
sector_scale |
Character: sector scale method. Default: "Origin", options: "Origin", "Scale". |
width_circle |
Numeric: outside circle width. Default: 3.0, min: 0.0, max: 10.0. |
dist_name |
Numeric: the distance of name and circle. Default: 3.0, min: 0.0, max: 10.0. |
label_dir |
Character: label director. Default: "Vertical", options: "Horizontal", "Vertical". |
dist_label |
Numeric: the distance of label and circle. Default: 0.3, min: 0.0. |
label_scale |
Numeric: labels font size sclae. Default: 0.8, min: 0, max: NULL. |
Plot: chord plot is used to visualize complex relationships between samples and genes, as well as between pathways and genes.
benben-miao
# 1. Library TOmicsVis package
library(TOmicsVis)
# 2. Use example dataset
data(gene_expression2)
head(gene_expression2)
# 3. Default parameters
chord_plot(gene_expression2[1:20,])
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