DotPlot_my: My enhanced DotPlot

In DawnEve/GEB: A R pkg to decorate Seurat output (single-cell RNA-seq tool)

My enhanced DotPlot

Description

version:0.1 add some colors

Usage

DotPlot_my(
  object,
  assay = NULL,
  features,
  cols = colorRampPalette(colors = c("lightyellow", "orangered", "red4"), bias = 0.5,
    interpolate = c("spline"))(100),
  col.min = -2.5,
  col.max = 2.5,
  dot.min = 0,
  dot.scale = 6,
  idents = NULL,
  group.by = NULL,
  split.by = NULL,
  cluster.idents = FALSE,
  scale = TRUE,
  scale.by = "radius",
  scale.min = NA,
  scale.max = NA,
  circle_size = 6,
  base_size = list(x = 14, y = 14, top = 14, legend = 14),
  rel_widths = c(1, 8),
  color_list = NULL
)

Arguments

object	Seurat obj
assay	which assay
features	gene list
cols	colors for expression
col.min	min?
col.max	max?
dot.min	dot min size
dot.scale	dot scale method
idents	which ident to show
group.by	group by
split.by	split by
cluster.idents	is cluster idents?
scale	scale?
scale.by	scale by?
scale.min	min?
scale.max	max?
base_size	font size list
rel_widths	relative widths
color_list	color list for each cluster

Examples

DotPlot_my(sce, features = c("CD3D", "CD79A"))
DotPlot_my(sce, features = c("CD3D", "CD79A"), cols = c("white", "red2"), rel_widths = c(1,4))
colors=c("#96C3D8", "#5F9BBE", "#F5B375", "#C0937E", "#67A59B", "#A5D38F", "#4A9D47", "#F19294", "#E45D61", "#3377A9",
"#BDA7CB", "#684797", "#8D75AF", "#CD9C9B", "#D62E2D", "#DA8F6F", "#F47D2F")
DotPlot_my(pbmc, features = split(top11$gene, top11$cluster), cols = c("white", "red3"), color_list=colors, rel_widths=c(1,45))
DotPlot_my(scObj_colon, features = common_markers, color_list = colors,
          rel_widths = c(1,35), base_size = list(legend=10, x=12))

DawnEve/GEB documentation built on July 6, 2022, 7:05 p.m.