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

benben-miao

Examples

# 1. Library TOmicsVis package
library(TOmicsVis)

# 2. Use example dataset
data(degs_lists)
head(degs_lists)
#>        CT.vs.LT20      CT.vs.LT15       CT.vs.LT12     CT.vs.LT12_6
#> 1 transcript_9024 transcript_4738  transcript_9956 transcript_10354
#> 2  transcript_604 transcript_6050  transcript_7601  transcript_2959
#> 3 transcript_3912 transcript_1039  transcript_5960  transcript_5919
#> 4 transcript_8676 transcript_1344  transcript_3240  transcript_2395
#> 5 transcript_8832 transcript_3069 transcript_10224  transcript_9881
#> 6   transcript_74 transcript_9809  transcript_3151  transcript_8836

# 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")