visualize: Visualize Proportionality

In propr: Calculating Proportionality Between Vectors of Compositional Data

Description

Visualize proportionality and differential proportionality.

Usage

## S4 method for signature 'propr,missing'
plot(x, y, prompt = TRUE, plotly = FALSE)

smear(rho, prompt = TRUE, plotly = FALSE)

dendrogram(rho, prompt = TRUE, plotly = FALSE)

bucket(rho, group, k, prompt = TRUE, plotly = FALSE)

prism(rho, k, prompt = TRUE, plotly = FALSE)

bokeh(rho, k, prompt = TRUE, plotly = FALSE)

pca(rho, group, prompt = TRUE, plotly = FALSE)

snapshot(rho, prompt = TRUE, plotly = FALSE)

cytescape(object, col1, col2, prompt = TRUE, d3 = FALSE)

propd2propr(object, ivar)

## S4 method for signature 'propd,missing'
plot(x, y, cutoff = 1000, col1, col2, propr,
  prompt = TRUE, d3 = FALSE, plotSkip = FALSE)

geyser(object, cutoff = 1000, k = 5, prompt = TRUE, plotly = FALSE)

bowtie(object, cutoff = 1000, k = 5, prompt = TRUE, plotly = FALSE)

gemini(object, cutoff = 1000, k = 5, prompt = TRUE, plotly = FALSE)

decomposed(object, cutoff = 1000)

parallel(object, cutoff = 1000, include = NA, or = TRUE,
  plotly = FALSE)

Arguments

x	A propr or propd object.
y	Missing. Ignore. Leftover from the generic method definition.
prompt	A logical scalar. Set to FALSE to disable the courtesy prompt when working with big data.
plotly	A logical scalar. Set to TRUE to produce a dynamic plot using the plotly package.
rho	A propr or propd object.
group	A character vector. Group or sub-group memberships, ordered according to the row names in counts.
k	An integer. For propr methods, the number of co-clusters (where all pairs receive a specified color if and only if both members belong to same the cluster). For propd methods, the maximum number of PALs to index when calculating pals in the network.
object	A propr or propd object.
col1	A character vector. Specifies which nodes to color red or blue, respectively.
col2	A character vector. Specifies which nodes to color red or blue, respectively.
d3	A boolean. Use rgl to plot 3D network.
ivar	A numeric scalar. Specifies reference feature(s) for additive log-ratio transformation. The argument will also accept feature name(s) instead of the index position(s). Set to "iqlr" to use inter-quartile log-ratio transformation. Ignore to use centered log-ratio transformation.
cutoff	For updateCutoffs, a numeric vector. this argument provides the FDR cutoffs to test. For graph functions, a numeric scalar. This argument indicates the maximum theta to include in the figure. For graph functions, a large integer will instead retrieve the top N pairs as ranked by theta.
propr	A propr or propd object.
plotSkip	A boolean. Toggles whether to build the network graph without plotting it. Used by pals.
include	This argument indicates which features by name should belong to a pair for that pair to get included in the results. Subset performed by Partner %in% subset | Pair %in% subset.
or	A boolean. If FALSE, include subsets by Partner %in% subset & Pair %in% subset.

propr Functions

plot: A wrapper for smear(x, ...).

smear: Plots log-ratio transformed abundances pairwise. Index-aware, meaning that it only plots pairs indexed in @pairs, unless no pairs are indexed. Returns a ggplot object.

dendrogram: Plots a clustering of the proportionality matrix. Index-aware, meaning that it only plots pairs indexed in @pairs, unless no pairs are indexed. Heatmap intensity is not scaled. Returns a dendrogram object.

bucket: Plots an estimation of the degree to which a feature pair differentiates the experimental groups versus the measure of the proportionality between that feature pair. The discrimination score is defined as the negative log of the p-values for each feature in the pair, computed independently using kruskal.test. "It's pronounced, 'bouquet'." - Hyacinth Bucket Returns cluster membership if k is provided. Otherwise, returns a ggplot object.

prism: Plots the variance of the ratio of the log-ratio transformed feature pair (VLR) versus the sum of the individual variances of each log-ratio transformed feature (VLS). The ratio of the VLR to the VLS equals 1 - rho. As such, we use here seven rainbow colored lines to indicate where rho equals [.01, .05, .50, 0, 1.50, 1.95, 1.99], going from red to violet. Returns cluster membership if k is provided. Otherwise, returns a ggplot object.

bokeh: Plots the feature variances for each log-ratio transformed feature pair in the propr object. Highly proportional pairs will aggregate near the y = x diagonal. Clusters that appear toward the top-right of the figure contain features with highly variable abundance across all samples. Clusters that appear toward the bottom-left of the figure contain features with fixed abundance across all samples. Uses a log scale. Returns cluster membership if k is provided. Otherwise, returns a ggplot object.

pca: Plots the first two principal components as calculated using the log-ratio transformed feature vectors. This provides a statistically valid alternative to conventional principal components analysis (PCA). For more information, see <DOI:10.1139/cjm-2015-0821>. Returns a ggplot object.

snapshot: Plots the log-ratio transformed feature abundance as a heatmap, along with the respective dendrograms. Heatmap intensity is not scaled. Returns a dendrogram object.

cytescape: Builds a table of indexed pairs and their proportionality. In doing so, this function displays a preview of the interaction network, built using igraph. We recommend using the result as input to a network visualization tool like Cytoscape. Returns a data.frame of indexed pairs.

propd Functions

propd2propr: Transforms a propd object into a propr object where the @matrix slot contains 1 - θ. Allows the user to interrogate theta using any visualization built for propr objects.

plot: Plots the interactions between pairs as a network. When plotting disjointed proportionality, red edges indicate that LRM1 > LRM2 while blue edges indicate that LRM1 < LRM2. When plotting emergent proportionality, red edges indicate that VLR1 < VLR2 while blue edges indicate that VLR1 > VLR2. Group labels numbered based on the order of the group argument to propd. Use col1 and col2 arguments to color nodes. For more control over the visualization of the network, consider exporting the table from shale to a network visualization tool like Cytoscape.

geyser: Plots indexed pairs based on the within-group log-ratio variance (VLR) for each group. Pairs near the origin show a highly proportional relationship in both groups. Each line away from the y = x line indicates a doubling of VLR compared to the other group. All pairs colored based on PAL (see: pals). See gemini.

bowtie: Plots indexed pairs based on the log-ratio means (LRM), relative to its PAL, for each group. Pairs near the origin show comparable LRM, relative to its PAL, in both groups. Each line away from the y = x line indicates a doubling of LRM compared to the other group. All pairs colored based on PAL (see: pals). See gemini.

gemini: Plots indexed pairs based on the log-fold difference in log-ratio variance (VLR) between the two groups versus the difference in log-ratio means (LRM). In this figure, the LRM for each group is signed (i.e., positive or negative) such that the PAL is the denominator of the log-ratio. This allows for a fluid comparison between pairs within the same PAL module. Pairs with a "Bridged" or "Missing" PAL get excluded from this graph. Remember that an increase in VLR suggests less proportionality. All pairs colored based on PAL (see: pals).

decomposed: Plots the decomposition of log-ratio variance into (weighted) group variances and between-group variance. Useful for visualizing how a theta type selects pairs.

parallel: Plots the sample-wise log-ratio abundance across all pairs selected by the provided cutoff. Use the reference argument to subset the plot to only include pairs that contain this reference.

propr documentation built on Dec. 16, 2019, 9:30 a.m.