VDJ_VJ_usage_circos: Makes a Circos plot from the VDJ_analyze output. Connects the...

In Platypus: Single-Cell Immune Repertoire and Gene Expression Analysis

Makes a Circos plot from the VDJ_analyze output. Connects the V gene with the corresponding J gene for each clonotype.

Description

Makes a Circos plot from the VDJ_analyze output. Connects the V gene with the corresponding J gene for each clonotype.

Usage

VDJ_VJ_usage_circos(
  VGM,
  VDJ.or.VJ,
  label.threshold,
  cell.level,
  c.threshold,
  clonotype.per.gene.threshold,
  c.count.label,
  c.count.label.size,
  platypus.version,
  filter1H1L,
  gene.label,
  gene.label.size,
  arr.col,
  arr.direction,
  topX,
  platy.theme,
  clonotype.column
)

Arguments

VGM	The output of the VDJ_build function has to be supplied. For Platypus v2: The output of the VDJ_GEX_integrate function (Platypus platypus.version v2). A list of data frames for each sample containing the clonotype information and cluster membership information.
VDJ.or.VJ	Determines whether to plot the V J gene pairing of the alpha or beta chain. "VDJ", "VJ" or "both" as possible inputs. Default: "both".
label.threshold	Genes are only labeled if the count is larger then the label.threshold. By default all label.threshold = 0 (all genes are labeled).
cell.level	Logical, defines whether weight of connection should be based on number of clonotypes of number of cells. Default: number of clonotypes.
c.threshold	Only clonotypes are considered with a frequency higher then c.threshold. Allows to filter for only highly expanded clonotypes.
clonotype.per.gene.threshold	How many clonotypes are required to plot a sector for a gene. Filters the rows and colums of the final adjacency matrix.
c.count.label	Boolean, lets the user decide if the gene and count labels should be plotted or not. Default = T.
c.count.label.size	Determines the font size of the gene labels. By default the font size for count labels is 0.6.
platypus.version	Which platypus.version of platypus is being used. Default = v3. Set to v3 if VDJ_GEX_matrix.output[[1]] is used
filter1H1L	Whether to filter the input VGM in "v3" to only include cells with 1 VDJ and 1 VJ chain. Defaults to TRUE
gene.label	Boolean, lets the user decide if the gene labels should be plotted or not.
gene.label.size	Determines the font size of the gene labels. By default the labelsize is automatically adjusted to 0.7 for labels with two or less digits, 0.6 for labels between 2 and 6 digits, and 0.4 for all longer labels. A manually defined font size will be the same for all labels!
arr.col	Data.frame with three columns where the first two indicate the names of genes, clonotypes or clusters to be connected, and the third corresponds to the color of the arrow. Default set to data.frame(c("dummy.clonotype"), c("dummy.cluster"), c("dummy.color")), so no arrow is drawn.
arr.direction	Either 1 or -1 and determines the direction of the arrow. Default=1.
topX	Filters for the top X clonotypes and only plots the respective gene combinations or cluster memberships.
platy.theme	Allows plotting in the new "pretty" theme or the older "spiky" theme without group labels and radial arrangement of gene.labels. Default = "pretty".
clonotype.column	Which column in VGM contains the clonotyping information? Default="clonotype_id_10X".

Value

Returns a circos plot and a list object with the following elememts for N samples: [[1 to N]] The first N listelements corresponds to the recorded circos plots for N beeing the number or samples in the VGM. Since Circlize uses the R base plotting funciton, this is not a ggplot object but can still be replotted by calling the first list element. [[N+1]] Adjacency matrix forwarded to VDJ_circos(). This Matrix contains the counts and can be used for manual replotting using VDJ_circos directly. [[N+2]] Contains a named list with colors for each connection drawn and can be used for manual replotting using VDJ_circos directly. [[N+3]] Contains a named list with grouping information and can be used for manual replotting using VDJ_circos directly.

Examples

 try({usage_circos_VDJVJ <- VDJ_VJ_usage_circos(Platypus::small_vdj)
 usage_circos_VDJVJ[[1]]
 })

Platypus documentation built on Oct. 18, 2024, 5:08 p.m.