tx_plot_metageneAtCDS | R Documentation |
Plot metagene at CDS
tx_plot_metageneAtCDS(
txDT,
geneAnnot,
colVars,
CDS_align,
upFlank,
doFlank,
summ_fun = "mean",
roll_fun = NULL,
roll_n = 100,
roll_align = "center",
roll_fill = NA,
smooth = TRUE,
spar = 0.3,
na.rm = TRUE,
normalize = FALSE,
tick_by = NULL
)
txDT |
data.table. A table as output by the |
geneAnnot |
GRanges. Gene annotation as loaded by |
colVars |
character. Names of columns for which values will be extracted |
CDS_align |
character. Either "start", "end", or "spliceSite" depending on the desired alignment, either to CDS start, CDS end, or splicing sites, respectively. |
upFlank |
numeric. Up-stream flank length |
doFlank |
numeric. Down-stream flank length |
summ_fun |
character. Summing function either "sum" or "mean". Default: "mean" |
roll_fun |
character. Rolling function either "sum" or "mean". Default: NULL |
roll_n |
numeric. Window size for rolling function |
roll_align |
character. Either "center" (default), "left" or "right" |
roll_fill |
vector. Either an empty vector (no fill), or a vector (recycled to) length 3 giving left, middle and right fills. NA by default |
smooth |
logical. Set to FALSE for not smoothing line. |
spar |
numeric. Smoothing parameter, typically (but not necessarily) in (0,1]. |
na.rm |
logical. Omit all NAs from computations. Default: TRUE |
normalize |
logical. If set to TRUE, values are normalized so that the area bellow the curve approximates to 1 for each variable. |
tick_by |
numeric. Distance between ticks in plot. Default: upFlank/2 |
ggplot
Smoothing function: smooth.spline
().
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