CumulativePlots: CumulativePlots

In fmi-basel/gbuehler-MiniChip: MiniChip

CumulativePlots

Description

Summarizes and plots the values for counts around positions of interest in the genome.

Usage

CumulativePlots(
  counts,
  bamNames = names(counts),
  span = 2025,
  step = 50,
  summarizing = "mean",
  overlapNames = "NA",
  plot = TRUE,
  confInterval = 0.95,
  plotcols = c("violet", "darkgrey"),
  overlapLabels = c("overlap", "no overlap")
)

Arguments

counts	A list of counts across peak summits generated by SummitHeatmap.
bamNames	Character vector containing the names to describe the bamFiles you are using (for example: "H3K9me3_reads"). If no names are supplied, the names of the counts list are used.
span	The distance from the peak summit to the left and right that you want your heatmap to extand to. Default is 2025.
step	The window size in which reads are counted/plotted in the heatmap. Default is 50.
summarizing	The function to summarize the heatmaps across peaks to achieve a cumulative line. Default is "mean".
overlapNames	A character vector of the row names of the counts that overlap with a given annotation, for example, transcription start sites.
plot	If TRUE (default), returns the cumulative plots, otherwise returns the underlying data table.
confInterval	The confidence interval around the mean that will be calculated and plotted. Default is .95. Only used if summarizing = "mean".
plotcols	Two different colors for the lines that contain the values for the peaks defined in overlapNames, and the rest of the peaks.
overlapLabels	Two different labels for the lines that contain the values for the peaks defined in overlapNames, and the rest of the peaks.

Details

This function plots summarized (default = mean) values of pre-calculated read counts around the positions of interest in the genome, for example summits of ChIP peaks.

Value

Returns a matrix with mean values of the log2 of supplied counts (with pseudocount of 1 added) in each bin for each sample, split by overlap_names. Plots of mean values for read counts around position of interest in the genome. One plot for each count matrix supplied. All plots are arranged on one page and saved as a png.

Examples

counts <- list(matrix(rnorm(21000,2,1),ncol=81,nrow=100,dimnames=list(1:100,-40:40)),
               matrix(rnorm(21000,2,1),ncol=81,nrow=100,dimnames=list(1:100,-40:40)))
bamNames <- c("counts1","counts2")
names(counts) <- bamNames
CumulativePlots(counts,bamNames=bamNames,overlapNames="NA")

fmi-basel/gbuehler-MiniChip documentation built on June 13, 2025, 6:15 a.m.