FbtPlot

Source code

Description

Generate Manhatten plot for log10 scaled p value for spatial dissimilarity test. X axis is the location of features. The function use ggplot2 as backend.

Usage

FbtPlot(
  object = NULL,
  val = NULL,
  assay = NULL,
  chr.name = "chr",
  start.name = "start",
  end.name = "end",
  col.by = NULL,
  cols = NULL,
  sel.chrs = NULL,
  pt.size = NULL,
  xlab = "Chromosome",
  ylab = expression(-log[10](p)),
  subset = NULL,
  point.label = NULL,
  label.size = 3,
  shape.by = NULL,
  chr = NULL,
  start = NULL,
  end = NULL,
  gtf = NULL,
  gene = NULL,
  upstream = 1000,
  downstream = 1000,
  print.genes = NULL,
  remove.chr = FALSE,
  layout.heights = c(3, 2)
)

Arguments

object Seurat object.
val Specify the name of p value. The name usually be format like bind-name.pval and bind-name.padj (BH adjusted p value). For example, if you use gene as binding feature, the name should be gene_name.pval or gene_name.padj.
assay Work assay.
chr.name The title of chromosome name in the meta table. Default is “chr”.
start.name The title of start position name in the meta table. Default is “start”.
end.name The title of end position name in the meta table. Default is “end”.
col.by Color points by specify the title of values in meta table. Can be discrete or continous.
cols Manually specify the colors. Used with col.by.
sel.chrs Vector of selected chromosome names to plot. Change the order by set the level of chr names.
pt.size Point size.
xlab Label for x axis. Default is “Chromosome”.
ylab Label for y axis. Default is “-log10p”.
subset Rule for subsetting the meta table before plot.
point.label Vector of points to plot their labels.
label.size Size of label. Default is 3.
shape.by Shape points by specify the title of values in meta table. Can only be discrete.
chr Choromsome to zoom in. Default is NULL, no zoom in. The zoom in mode can be enabled by setting chr or gene/gtf.
start Start position to zoom in.
end End position to zoom in.
gtf GTF database. Load by gtf2db. Default is NULL. If specified transcirpt tracks will be plotted.
gene Gene name to zoom in. Should used with gtf database specified.
upstream Flank zoom in region with upstream. Default is 1000. Only works when zoom in mode enabled.
downstream Flank zoom in region with downstream. Default is 1000. Only works when zoom in mode enabled.
print.genes Print the gene names in the transcript tracks. Default will print all or randomly 20 genes if more than 20 genes in this region.
remove.chr Remove ‘chr’ in the chromosome names.
layout.heights Specify the layouts for Manhatten plot and gene tracks. Default is c(3,2).
Back to top