spacedeconv/man/make_baseplot.Rd at d8ec20245ea19a9f1028f7c0937080f53e6646b2 · omnideconv/spacedeconv · GitHub

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
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/visualization.R
\name{make_baseplot}
\alias{make_baseplot}
\title{Render spatial hex plot}
\usage{
make_baseplot(
  spe,
  df,
  to_plot,
  palette = "Mako",
  transform_scale = NULL,
  sample_id = "sample01",
  reverse_palette = FALSE,
  image_id = "lowres",
  show_image = FALSE,
  background = NULL,
  zoom = TRUE,
  palette_type = NULL,
  offset_rotation = FALSE,
  spot_size = 1,
  limits = NULL,
  smooth = FALSE,
  smoothing_factor = 1.5,
  title_size = 30,
  title = NULL,
  font_size = 15,
  legend_size = 20,
  density = TRUE,
  save = FALSE,
  path = NULL,
  png_width = 1500,
  png_height = 750,
  show_legend = TRUE,
  nDigits = NULL,
  pseudocount = 1,
  shift_positive = TRUE,
  spot_shape = "hexagon"
)
}
\arguments{
\item{spe}{SpatialExperiment with deconvolution results}

\item{df}{containing the annotation to be plotted}

\item{to_plot}{column of df to plot}

\item{palette}{colorspace palette (sequential)}

\item{transform_scale}{data transform_scaleation to use, "log"}

\item{sample_id}{sample of the SpatialExperiment to be plotted}

\item{reverse_palette}{reverse color palette}

\item{image_id}{image id for background image}

\item{show_image}{whether to show the spatial image}

\item{background}{custom background color}

\item{zoom}{zoom to the available spots}

\item{palette_type}{"discrete", "sequential", "diverging"}

\item{offset_rotation}{correct hex orientation for rotated visium image}

\item{spot_size}{increase (>1) or decrease (<1) the hex size}

\item{limits}{vector of color scale limits}

\item{smooth}{whether to smooth the plot}

\item{smoothing_factor}{kernel size factor (multiples of spot distance)}

\item{title_size}{font size of title}

\item{title}{set a custom title}

\item{font_size}{font size of legend}

\item{legend_size}{legend size in points}

\item{density}{whether to display a density distribution next to the spatial plot}

\item{save}{set TRUE to save plot}

\item{path}{specify directory to save plot, if NULL: saving at ~/spacedeconv}

\item{png_width}{when saving, png width in px}

\item{png_height}{when saving, png height in px}

\item{show_legend}{whether to show the legend}

\item{nDigits}{Round Values, Number of Digits after the comma}
}
\description{
Render spatial hex plot
}