DynamicPlot: DynamicPlot
In zh542370159/SCP: Single Cell Pipeline

DynamicPlot

R Documentation

DynamicPlot

Description

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.

Examples

data("pancreas_sub")
pancreas_sub <- RunSlingshot(pancreas_sub, group.by = "SubCellType", reduction = "UMAP")
CellDimPlot(pancreas_sub, group.by = "SubCellType", reduction = "UMAP", lineages = paste0("Lineage", 1:3), lineages_span = 0.1)
DynamicPlot(
  srt = pancreas_sub,
  lineages = "Lineage1",
  features = c("Nnat", "Irx1", "G2M_score"),
  group.by = "SubCellType",
  compare_features = TRUE
)
DynamicPlot(
  srt = pancreas_sub,
  lineages = c("Lineage1", "Lineage2"),
  features = c("Nnat", "Irx1", "G2M_score"),
  group.by = "SubCellType",
  compare_lineages = TRUE,
  compare_features = FALSE
)
DynamicPlot(
  srt = pancreas_sub,
  lineages = c("Lineage1", "Lineage2"),
  features = c("Nnat", "Irx1", "G2M_score"),
  group.by = "SubCellType",
  compare_lineages = FALSE,
  compare_features = FALSE
)

zh542370159/SCP documentation built on Nov. 22, 2023, 2:34 a.m.