plot_feature_sample_mat: Plot a Feature-Sample Matrix
In tinyheero/tinyutils: Utility Functions to Assist With Data Analysis

Description Usage Arguments Examples

Generates a ggplot2::geom_tile plot of features by sample. It is able to deal with multiple types affecting the same sample.

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plot_feature_sample_mat(in.df, feature.order, sample.id.order, fill.colors,
  type.display.mode = c("multiple", "single"), type.order, tile.col = NA,
  rotate.x.labels, missing.fill.col)

`in.df`	A 3 column (feature, sampleID, type) data.frame object
`feature.order`	character vector indicating the order of the features in the final plot on the y-axis. If not set, then function will set it automatically
`sample.id.order`	character vector indicating the order of the samples in the final plot on the x-axis. If not set, then function will set it automatically
`fill.colors`	character vector indicating the colors of the different "types". The names should be the types with the value being the color
`type.display.mode`	Specify whether multiple or a single feature type can appear in the same feature/sample cell
`type.order`	Specify the "priority" of the feature types. This only has an effect when type.display.mode is set to single
`tile.col`	Border color of each cell. If not yet, no border color is used
`rotate.x.labels`	Rotate the x-axes labels by a certain degree
`missing.fill.col`	Color of the cell that has missing values

v1 <- c("RCOR1", "NCOR1", "LCOR", "RCOR1", "RCOR1", "RCOR1", "RCOR1")
v2 <- c("sampleA", "sampleC", "sampleB", "sampleC", "sampleA", "sampleC", "sampleC")
v3 <- c("Deletion", "Deletion", "SNV", "Rearrangement", "SNV", "Rearrangement", "SNV")
feature.order <- c("RCOR1", "NCOR1", "LCOR")
sample.id.order <- c("sampleA", "sampleB", "sampleC")
in.df <- dplyr::data_frame(feature = v1, sampleID = v2, type = v3)
fill.colors <- c("Deletion" = "Blue", "Rearrangement" = "Green", "SNV" = "Red")

plot_feature_sample_mat(in.df)

# With black tile color
plot_feature_sample_mat(in.df, tile.col = "black")

# Fill in missing values with a lightgrey color
plot_feature_sample_mat(in.df, tile.col = "black", 
  missing.fill.col = "lightgrey")

# Rotate x-axes labels by 90 degrees
plot_feature_sample_mat(in.df, rotate.x.labels = 90)

# Specify order of features, samples, and colors
plot_feature_sample_mat(in.df, feature.order, sample.id.order, 
  fill.colors = fill.colors)

# Specify each cell can only have one "feature type"
plot_feature_sample_mat(in.df, feature.order, sample.id.order, fill.colors = fill.colors,
  type.display.mode = "single")

# Specify the specific priority of the "feature type" for cells with
# multiple features
plot_feature_sample_mat(in.df, feature.order, sample.id.order, fill.colors = fill.colors,
  type.display.mode = "single", type.order = c("Rearrangement", "SNV", "Deletion"))