heatMapL {ORFik} | R Documentation |
Coverage heatmap of multiple libraries
heatMapL( region, tx, df, outdir, scores = "sum", upstream, downstream, zeroPosition = upstream, acceptedLengths = NULL, type = "ofst", legendPos = "right", colors = "default", addFracPlot = TRUE, location = "TIS", shifting = NULL, skip.last = FALSE, format = ".png", plot.together = TRUE, title = TRUE )
region |
#' a |
tx |
default NULL, a GRangesList of transcripts or (container region), names of tx must contain all grl names. The names of grl can also be the ORFik orf names. that is "txName_id" |
df |
an ORFik |
outdir |
a character path to directory to save plot, will be named from ORFik experiment columns |
scores |
character vector, default c("transcriptNormalized", "sum"), either of zscore, transcriptNormalized, sum, mean, median, .. see ?coverageScorings for info and more alternatives. |
upstream |
1 or 2 integers, default c(50, 30), how long upstream from 0 should window extend (first index is 5' end extension, second is 3' end extension). If only 1 shifting, only 1 value should be given, if two are given will use first. |
downstream |
1 or 2 integers, default c(29, 69), how long upstream from 0 should window extend (first index is 5' end extension, second is 3' end extension). If only 1 shifting, only 1 value should be given, if two are given will use first. |
zeroPosition |
an integer DEFAULT (upstream), what is the center point? Like leaders and cds combination, then 0 is the TIS and -1 is last base in leader. NOTE!: if windows have different widths, this will be ignored. |
acceptedLengths |
an integer vector (NULL), the read lengths accepted. Default NULL, means all lengths accepted. |
type |
character, default: "ofst". Type of library: either "default", usually bam format (the one you gave to experiment), "pshifted" pshifted reads, "ofst", "bed", "bedo" optimized bed, or "wig" |
legendPos |
a character, Default "right". Where should the fill legend be ? ("top", "bottom", "right", "left") |
colors |
character vector, default: "default", this gives you: c("white", "yellow2", "yellow3", "lightblue", "blue", "navy"), do "high" for more high contrasts, or specify your own colors. |
addFracPlot |
Add margin histogram plot on top of heatmap with fractions per positions |
location |
a character, default "start site", will make xlabel of heatmap be Position relative to "start site" or alternative given. |
shifting |
a character, default c("5prime", "3prime"), can also be either or NULL (no shifting of reads) |
skip.last |
skip top(highest) read length, default FALSE |
format |
a character, default ".png", alternative ".pdf" |
plot.together |
logical (default: FALSE), plot all in 1 plot (if TRUE) |
title |
a character, default NULL (no title), what is the top title of plot? |
invisible(NULL), plots are saved
Other heatmaps:
coverageHeatMap()
,
heatMapRegion()
,
heatMap_single()