barcode_ggheatmap: barcode_ggheatmap (Barcode Heatmap using ggplot2)

Description Usage Arguments Value Examples

View source: R/barcode_ggheatmap.R

Description

Creates a heatmap using the top 'n' rows from each column, using ggplot2!

Usage

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barcode_ggheatmap(your_data, names = colnames(your_data), n_clones = 10,
  your_title = "", grid = TRUE, label_size = 1, dendro = FALSE,
  cellnote_size = 4, printtable = FALSE, table_option = "percents",
  log_transform = TRUE, log_choice = exp(1),
  distance_method = "Euclidean", minkowski_power = 1,
  cellnote_option = "stars", hclust_linkage = "complete",
  row_order = "hierarchical", clusters = 0)

Arguments

your_data

A data frame. Usually individual barcodes in rows and samples in columns.

names

Vector of x axis labels.

n_clones

The top 'n' clones to plot.

your_title

The title for the plot.

grid

Logical. Include a grid or not in the heatmap.

label_size

The size of the column labels.

dendro

Logical. Whether or not to show row dendrogram for hierarchical clustering.

cellnote_size

The numerical size of the cell note labels.

printtable

Logical. Prints percent contribution as a table instead of plotting it.

table_option

Character. One of "logs", "reads", or "percents" for printing.

log_transform

Logical. Log transform data before clustering and plotting.

log_choice

Data is log transformed with this log.

distance_method

Character. Use summary(proxy::pr_DB) to see all options.

minkowski_power

The power of the Minkowski distance (if minkowski is used).

cellnote_option

Character. One of "stars", "reads", or "percents"

hclust_linkage

Character. One of one of "ward.D", "ward.D2", "single", "complete", "average" (= UPGMA), "mcquitty" (= WPGMA), "median" (= WPGMC) or "centroid" (= UPGMC).

row_order

Character. One of "hierarchical" or "emergence" to organize rows.

clusters

How many clusters to cut hierarchical tree into for display when row_order is "hierarchical".

Value

Displays a heatmap in the current plot window.

Examples

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BCheatmap(your_data = zh33, names = colnames(zh33), n_clones = 10,
      your_title = "First Time Point", grid = TRUE, columnLabels = 3)
BCheatmap(your_data = zh33, n_clones = 10, printtable = TRUE)

truittll/barcodetrackPython documentation built on Nov. 18, 2017, 11:19 p.m.