Skip to contents

DynamicPlot

Source: R/SCP-plot.R
DynamicPlot.Rd

Plot dynamic features across pseudotime.

Usage

DynamicPlot(
  srt,
  lineages,
  features,
  group.by = NULL,
  cells = NULL,
  slot = "counts",
  assay = NULL,
  family = NULL,
  exp_method = c("log1p", "raw", "zscore", "fc", "log2fc"),
  lib_normalize = identical(slot, "counts"),
  libsize = NULL,
  compare_lineages = TRUE,
  compare_features = FALSE,
  add_line = TRUE,
  add_interval = TRUE,
  line.size = 1,
  line_palette = "Dark2",
  line_palcolor = NULL,
  add_point = TRUE,
  pt.size = 1,
  point_palette = "Paired",
  point_palcolor = NULL,
  add_rug = TRUE,
  flip = FALSE,
  reverse = FALSE,
  x_order = c("value", "rank"),
  aspect.ratio = NULL,
  legend.position = "right",
  legend.direction = "vertical",
  theme_use = "theme_scp",
  theme_args = list(),
  combine = TRUE,
  nrow = NULL,
  ncol = NULL,
  byrow = TRUE,
  seed = 11
)

Arguments

srt

A Seurat object.

lineages

A character vector specifying the lineages to plot.

features

A character vector specifying the features to plot.

group.by

A character specifying a metadata column to group the cells by. Default is NULL.

cells

A character vector specifying the cells to include in the plot. Default is NULL.

slot

A character string specifying the slot to use for the analysis. Default is "counts".

assay

A character string specifying the assay to use for the analysis. Default is NULL.

family

A character specifying the model used to calculate the dynamic features if needed. By default, this parameter is set to NULL, and the appropriate family will be automatically determined.

exp_method

A character specifying the method to transform the expression values. Default is "log1p" with options "log1p", "raw", "zscore", "fc", "log2fc".

lib_normalize

A boolean specifying whether to normalize the expression values using library size. By default, if the slot is counts, this parameter is set to TRUE. Otherwise, it is set to FALSE.

libsize

A numeric vector specifying the library size for each cell. Default is NULL.

compare_lineages

A boolean specifying whether to compare the lineages in the plot. Default is TRUE.

compare_features

A boolean specifying whether to compare the features in the plot. Default is FALSE.

add_line

A boolean specifying whether to add lines to the plot. Default is TRUE.

add_interval

A boolean specifying whether to add confidence intervals to the plot. Default is TRUE.

line.size

A numeric specifying the size of the lines. Default is 1.

line_palette

A character string specifying the name of the palette to use for the line colors. Default is "Dark2".

line_palcolor

A vector specifying the colors to use for the line palette. Default is NULL.

add_point

A boolean specifying whether to add points to the plot. Default is TRUE.

pt.size

A numeric specifying the size of the points. Default is 1.

point_palette

A character string specifying the name of the palette to use for the point colors. Default is "Paired".

point_palcolor

A vector specifying the colors to use for the point palette. Default is NULL.

add_rug

A boolean specifying whether to add rugs to the plot. Default is TRUE.

flip

A boolean specifying whether to flip the x-axis. Default is FALSE.

reverse

A boolean specifying whether to reverse the x-axis. Default is FALSE.

x_order

A character specifying the order of the x-axis values. Default is c("value", "rank").

aspect.ratio

A numeric specifying the aspect ratio of the plot. Default is NULL.

legend.position

A character string specifying the position of the legend in the plot. Default is "right".

legend.direction

A character string specifying the direction of the legend in the plot. Default is "vertical".

theme_use

A character string specifying the name of the theme to use for the plot. Default is "theme_scp".

theme_args

A list specifying the arguments to pass to the theme function. Default is list().

combine

A boolean specifying whether to combine multiple plots into a single plot. Default is TRUE.

nrow

A numeric specifying the number of rows in the combined plot. Default is NULL.

ncol

A numeric specifying the number of columns in the combined plot. Default is NULL.

byrow

A boolean specifying whether to fill plots by row in the combined plot. Default is TRUE.

seed

A numeric specifying the random seed. Default is 11.

See also

RunDynamicFeatures

Examples

data("pancreas_sub")
pancreas_sub <- RunSlingshot(pancreas_sub, group.by = "SubCellType", reduction = "UMAP")
#> Warning: No shared levels found between `names(values)` of the manual scale and the data's fill values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the data's fill values.
#> Warning: Removed 8 rows containing missing values or values outside the scale range (`geom_path()`).
#> Warning: Removed 8 rows containing missing values or values outside the scale range (`geom_path()`).
#> Error in gtable_add_grob(gtable, grob, t = mean(gtable$layout[grep("panel",     gtable$layout$name), "t"]), l = dim(gtable)[2], clip = clip): `grobs` must be a single grob or a list of grobs, not a list matrix.
CellDimPlot(pancreas_sub, group.by = "SubCellType", reduction = "UMAP", lineages = paste0("Lineage", 1:3), lineages_span = 0.1)
#> Error in CellDimPlot(pancreas_sub, group.by = "SubCellType", reduction = "UMAP",     lineages = paste0("Lineage", 1:3), lineages_span = 0.1): Lineage1 is not in the meta.data of srt object.
DynamicPlot(
  srt = pancreas_sub,
  lineages = "Lineage1",
  features = c("Nnat", "Irx1", "G2M_score"),
  group.by = "SubCellType",
  compare_features = TRUE
)
#> Error in check_R("MatrixGenerics"): could not find function "check_R"
DynamicPlot(
  srt = pancreas_sub,
  lineages = c("Lineage1", "Lineage2"),
  features = c("Nnat", "Irx1", "G2M_score"),
  group.by = "SubCellType",
  compare_lineages = TRUE,
  compare_features = FALSE
)
#> Error in check_R("MatrixGenerics"): could not find function "check_R"
DynamicPlot(
  srt = pancreas_sub,
  lineages = c("Lineage1", "Lineage2"),
  features = c("Nnat", "Irx1", "G2M_score"),
  group.by = "SubCellType",
  compare_lineages = FALSE,
  compare_features = FALSE
)
#> Error in check_R("MatrixGenerics"): could not find function "check_R"