ssvFeatureBinaryHeatmap: ssvFeatureBinaryHeatmap

In jrboyd/seqsetvis: Set Based Visualizations for Next-Gen Sequencing Data

ssvFeatureBinaryHeatmap

Description

Outputs a ggplot binary heatmap, where color indicates TRUE and the other indicates FALSE in a membership table. The heatmap is sorted, TRUE at the top, by column left to right. Changes to column order can reveal different patterns.

Usage

ssvFeatureBinaryHeatmap(
  object,
  raster_approximation = TRUE,
  true_color = "black",
  false_color = "#EFEFEF",
  raster_width_min = 1000,
  raster_height_min = 1000,
  return_data = FALSE
)

Arguments

object	passed to ssvMakeMembTable
raster_approximation	If TRUE, instead of standard ggplot, write temporary raster png image and redraw that as plot background. default is FALSE
true_color	character. rcolor or hex color used for TRUE values. default is "black".
false_color	character. rcolor or hex color used for TRUE values. default is "#EFEFEF", a gray.
raster_width_min	raster width will be minimum multiple of number of columns over this number. ignored if raster_approximation is FALSE.
raster_height_min	raster height will be minimum multiple of number of rows over this number ignored if raster_approximation is FALSE
return_data	logical. If TRUE, return value is no longer ggplot and is instead the data used to generate that plot. Default is TRUE

Details

As a svg output, the final plot can be unwieldy. The default of raster_approximation = TRUE is easier to work with, especially for larger membership tables.

Value

ggplot using geom_tile of membership table sorted from left to right.

Examples

data(CTCF_in_10a_overlaps_gr)
ssvFeatureBinaryHeatmap(list(1:3, 2:6))
# horizontal version
ssvFeatureBinaryHeatmap(list(1:3, 2:6)) + coord_flip() +
  theme(axis.text.x = element_blank(), axis.text.y = element_text())
ssvFeatureBinaryHeatmap(CTCF_in_10a_overlaps_gr)
ssvFeatureBinaryHeatmap(S4Vectors::mcols(CTCF_in_10a_overlaps_gr)[,2:3])
ssvFeatureBinaryHeatmap(S4Vectors::mcols(CTCF_in_10a_overlaps_gr)[,3:2])

jrboyd/seqsetvis documentation built on Sept. 15, 2024, 1:11 a.m.