plot_MultiSpp: Plot MultiSpp co-appearance matrix

Description Usage Arguments Author(s) See Also Examples

View source: R/functions.R

Description

Plot co-appearance heatmap of co-expression network generated across multiple species

Usage

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plot_MultiSpp(GeneMeta,order,CA_keep,sb=12, remove_0=TRUE,
    text_rotate=NULL, lwd=0.5, cex=0.2,
    my_palette=colorRampPalette(c("white", "lightyellow", "red","black"))(n = 100))

Arguments

GeneMeta

Data frame that contains the project metadata. See createGeneMeta

order

The order in which genes should be plotted.

CA_keep

Sparse matrix of louvain community assignments generated from many runs of louvain

sb

An integer specifying the increment of the sequence to plot. Example plots every 12th gene in the order.

remove_0

A logical value indicating if the unclusterable genes should be plotted.

text_rotate

Angle of module labels.

lwd

Line weight

cex

Font proportion

my_palette

Specify your own color ramp for the heatmap

Author(s)

Matthew Zinkgraf, [email protected]

See Also

cluster_louvain

Examples

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data("GeneMeta")
data("occurance")
data("MultiSppTrees")
plot_MultiSpp(GeneMeta = GeneMeta, order = MultiSpp_trees$order,
      sb=12, CA_keep = occurance, remove_0 = F, lwd = 1, cex = 0.5)

mzinkgraf/fastOC documentation built on Aug. 15, 2018, 11:17 p.m.