stsPlotSummaryProfiles: stsPlotSummaryProfiles

In jrboyd/seqtsne: Application of t-sne to NGS Genomic Signal Profiles

stsPlotSummaryProfiles

Description

stsPlotSummaryProfiles

Usage

stsPlotSummaryProfiles(
  profile_dt,
  position_dt,
  x_points,
  y_points = x_points,
  x_var = "x",
  y_var = "y",
  extra_vars = character(),
  id_var = "id",
  wide_var = "name",
  tall_var = "tall_none",
  q_tall_values = NULL,
  q_wide_values = NULL,
  xrng = NULL,
  yrng = NULL,
  plot_type = c("glyph", "raster")[1],
  rname = NULL,
  odir = NULL,
  force_rewrite = FALSE,
  n_cores = getOption("mc.cores", 1),
  apply_norm = TRUE,
  ylim = c(0, 1),
  ma_size = 2,
  n_splines = 10,
  p = NULL,
  facet_byCell = FALSE,
  line_color_mapping = NULL,
  vertical_facet_mapping = NULL,
  N_floor = 0,
  N_ceiling = NULL,
  min_size = 0.3,
  return_data = FALSE
)

Arguments

profile_dt	a tidy data.table for profile data as retrieved by stsFetchTsneInput. Expected variable names are id, tall_var, wide_var, x, and y.
position_dt	a tidy data.table containing t-sne embedding. Expected variable names are tx, ty, id, and tall_var.
x_points	numeric. number of grid points to use in x dimension.
y_points	numeric. number of grid points to use in y dimension. Defaults to same value as x_points.
xrng	view domain in x dimension, default is range of position_dt$tx.
yrng	view domain in y dimension, default is range of position_dt$ty.
plot_type	character, must be one of "glyph" or "raster". raster uses ggimage::geom_image to embed images where glyph uses GGally::glyphs
rname	prefix for image files. existing image files are used if present.
odir	output directory for image files.
force_rewrite	if TRUE, images are overwritten even if they exist.
n_cores	number of cores to use when writing images. Default is value of mc.cores option if set or 1.
apply_norm	if TRUE, y values are trimmed to 95th percentile and transformed ot domain of [0,1]. Default is TRUE.
ylim	y-limits of regional summary plots. Default of c(0, 1) is compatible with apply_norm = TRUE.
ma_size	moving average size when smoothing profiles.
n_splines	number of points to interpolate with splines.
p	an existing ggplot to overlay images onto. Default of NULL starts a new plot.
facet_byCell	boolean. If TRUE, plots are facetted by tall_var.
line_color_mapping	named vector of line color. Names correspond to values of profile_dt 'wide_var' variable and values are colors.
vertical_facet_mapping	named vector of groups. vertical_facet_mapping names are wide_vars and order of first occurence determines vertical position top to bottom.
N_floor	The value of N to consider 0. bins with N values <= N_floor will be ignored.
N_ceiling	The value of N to consider 1. bins with N values >= N_ceiling will have images drawn at full size.
min_size	Numeric (0, 1]. The minimum size images to draw. The default of .3 draws images for all bins with N values >= 30 N_floor to N_ceiling.
return_data	if TRUE, data.table that would have been used to create ggplot is returned instead.
q_tall_vars	character vector of tall_vars to plot. Default of NULL plots all.
q_wide_vars	character vector of wide_vars to plot. Default of NULL plots all.

Value

returns a ggplot containing images summarizing t-sne space at resolution determined by x_points and y_points with the space density mapped to size.

Examples

data("profile_dt")
data("tsne_dt")
stsPlotSummaryProfiles(profile_dt, tsne_dt, x_points = 4)

jrboyd/seqtsne documentation built on Nov. 5, 2022, 6:37 a.m.