upsetr_plot {TOmicsVis} | R Documentation |
UpSet plot for stat common and unique gene among multiple sets.
Description
UpSet plot for stat common and unique gene among multiple sets.
Usage
upsetr_plot(
data,
sets_num = 4,
keep_order = FALSE,
order_by = "freq",
decrease = TRUE,
mainbar_color = "#006600",
number_angle = 45,
matrix_color = "#cc0000",
point_size = 4.5,
point_alpha = 0.5,
line_size = 0.8,
shade_color = "#cdcdcd",
shade_alpha = 0.5,
setsbar_color = "#000066",
setsnum_size = 6,
text_scale = 1.2
)
Arguments
data |
Dataframe: Paired comparisons differentially expressed genes (degs) among groups (1st-col~: degs of paired comparisons). |
sets_num |
Numeric: sets number. Default: 4, min: 2, max: NULL. |
keep_order |
Logical: keep sets in the order entered using the sets parameter. Default: FALSE, options: TRUE, FALSE. |
order_by |
Character: intersections in the matrix should be ordered by. Default: "freq" (frequency), options: "freq", "degree", "both". |
decrease |
Logical: order by decrease. Default: TRUE, options: TRUE, FALSE. |
mainbar_color |
Charactor: mainbar color (color name or hex value). Default: "#006600". |
number_angle |
Numeric: number display angle. Default: 45, min: 0, max: 360. |
matrix_color |
Charactor: matrix point color (color name or hex value). Default: "#cc0000". |
point_size |
Numeric: point size. Default: 4.5, min: 0.0, max: NULL. |
point_alpha |
Numeric: point color alpha. Default: 0.50, min: 0.00, max: 1.00. |
line_size |
Numeric: connection line size. Default: 0.8, min: 0.00, max: NULL. |
shade_color |
Character: matrix shade color. Default: "#cdcdcd". |
shade_alpha |
Numeric: shade color alpha. Default: 0.50, min: 0.00, max: 1.00. |
setsbar_color |
Character: sets bar color. Default: "#000066". |
setsnum_size |
Numeric: sets bar number size. Default: 6. |
text_scale |
Numeric: all text scale. Default: 1.2, min: 0.01, max: NULL. |
Value
Plot: UpSet plot for stat common and unique gene among multiple sets.
Author(s)
benben-miao
Examples
# 1. Library TOmicsVis package
library(TOmicsVis)
# 2. Use example dataset
data(degs_lists)
head(degs_lists)
# 3. Default parameters
upsetr_plot(degs_lists)
# 4. Set keep_order = TRUE, order_by = "degree"
upsetr_plot(degs_lists, keep_order = TRUE, order_by = "degree")
# 5. Set mainbar_color = "#333333", number_angle = 0
upsetr_plot(degs_lists, mainbar_color = "#333333", number_angle = 0)
# 6. Set shade_color = "#ffcc00", setsbar_color = "#0000cc"
upsetr_plot(degs_lists, shade_color = "#ffcc00", setsbar_color = "#0000cc")