PlotCoverageByGroup: Plot scATACseq coverage for each cluster from tabix indexed...
In crazyhottommy/scATACutils: What the Package Does (One Line, Title Case)

Description Usage Arguments Value Examples

reads in the fragments.tsv.gz or bam file for only the given region (gene), and plot using karyoploteR package

PlotCoverageByGroup(chrom = NULL, start = NULL, end = NULL,
  gene_name = NULL, upstream = 2000, downstream = 2000,
  fragment = NULL, bam = NULL, cellbarcode_tag = "CB",
  mapqFilter = 30, grouping, clusters_to_plot = NULL,
  genome = "hg19", txdb = TxDb.Hsapiens.UCSC.hg19.knownGene,
  eg.db = org.Hs.eg.db, ymax = NULL, label_cex = 1,
  label_side = "left", label.margin = 0.05, yaxis_cex = 1,
  track_cols = "cadetblue2", tick.dist = 10000,
  minor.tick.dist = 2000, tick_label_cex = 1)

`chrom`	chromosome
`start`	chromosome start
`end`	chromosome end
`gene_name`	gene symbol for the gene one want's to plot. e.g. VEGFA. Use either chrom, start, end or gene_name
`upstream`	If use gene_name, specify the upstream bp for extending the GRanges
`downstream`	If use gene_name, specify the downstream bp for extending the GRanges
`fragment`	path to the fragment.tsv.gz file from 10x cellranger-atac output. indexed by tabix.
`bam`	path to the bam file
`cellbarcode_tag`	The cell barcode tag in the bam file, default is "CB" as in the 10x output
`mapqFilter`	the mapq quality score filter for reads from bam file, default is 30,
`grouping`	path to a tsv file with three columns: "cell", "cluster", "depth". "cell" is the cell barcode, "cluster" is the cluster id for each cell, and "depth" is the number of reads in that cell.
`clusters_to_plot`	A character vector containing clusters to plot in the tracks from bottom to top. default is all clusters
`genome`	hg19, hg38 or mm9, mm10
`txdb`	A TxDb object, e.g. TxDb.Hsapiens.UCSC.hg19.knownGene
`eg.db`	Either org.Hs.eg.db or org.Mm.eg.db
`ymax`	ymax for each track, if not specified, max of all the tracks will be calculated. Every track will use the same ymax, so it is comparable across clusters.
`label_cex`	size of the cluster label
`label_side`	side of the cluster label. "left" or "right".
`label.margin`	the position of the cluster label, sepcify negative e.g., -0.6 to move to the center of the track body if label_side is left.
`yaxis_cex`	size of the y-axis
`track_cols`	a vector of colors for the tracks, should be the same length as clusters_to_plot or the total number of clusters. If clusters_to_plot is NULL, and track_cols has only one element, all tracks will be plotted with the same color.
`tick.dist`	chromosome tick distance to mark, default 10kb
`minor.tick.dist`	minor chromosome tick distance to mark, default 2000 bp
`tick_label_cex`	size of the tick label

A karyoploteR object

## Not run: 
library(org.Hs.eg.db)
library(org.Mm.eg.db)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(TxDb.Mmusculus.UCSC.mm10.knownGene)
chrom<-  "chr12"
start<-  69730394
end<- 69760971
plotCoverageByGroup(chrom = chrom, start = start, end = end, fragment = "data/atac_viz/10k_pbmc/atac_v1_pbmc_10k_fragments.tsv.gz",
                    grouping = "data/atac_viz/grouping.txt", track_cols = "red")
plotCoverageByGroup(gene_name = "NKG7", fragment = "data/atac_viz/10k_pbmc/atac_v1_pbmc_10k_fragments.tsv.gz",
                    grouping = "data/atac_viz/grouping.txt", tick_label_cex = 1, tick.dist = 5000,
                    minor.tick.dist = 1000)

plotCoverageByGroup(gene_name = "NKG7", fragment = "data/atac_viz/10k_pbmc/atac_v1_pbmc_10k_fragments.tsv.gz",
                    grouping = "data/atac_viz/grouping.txt", tick_label_cex = 1, tick.dist = 5000,
                    minor.tick.dist = 1000, track_cols = c("red", "blue", ""cadetblue2"),
                    clusters_to_plot = c("1", "3, "4"))

plotCoverageByGroup(gene_name = "NKG7", bam = "data/atac_viz/10k_pbmc/atac_v1_pbmc_10k.bam",
                    cellbarcode_tag= "CB", mapqFilter = 30,
                    grouping = "data/atac_viz/grouping.txt", tick_label_cex = 1, tick.dist = 5000,
                    minor.tick.dist = 1000)

## End(Not run)