TEMPTED Vignette

Introduction of TEMPTED

This is a vignette for the R package tempted, which implements the statistical method TEMPoral TEnsor Decomposition (TEMPTED). The goal of TEMPTED is to perform dimensionality reduction for multivariate longitudinal data, with a special attention to longitudinal mirobiome studies.

Package dependencies: R (>= 4.2.0), np (>= 0.60-17), ggplot2 (>= 3.4.0), methods (>= 4.2.1).

Run time for all the example codes in this demo was within one minute on a MacBook Pro with 2.3 GHz Intel Core i7 processor. You may expect longer run time if you have more subjects or more features.

You can cite this paper for using TEMPTED:

Shi P, Martino C, Han R, Janssen S, Buck G, Serrano M, Owzar K, Knight R, Shenhav L, Zhang AR. Time-Informed Dimensionality Reduction for Longitudinal Microbiome Studies. bioRxiv.

The statistical theories behind TEMPTED can be found in this paper:

Han R, Shi P, Zhang AR. Guaranteed Functional Tensor Singular Value Decomposition. Journal of the American Statistical Association (2023): 1-13.

TEMPTED is also implemented in Python through the Python package gemelli and as a plugin of Qiime2. It can be installed through pip install gemelli. Documentation for gemelli.

Installation

You can directly install TEMPTED from CRAN by

install.packages("tempted")

Typical installation time is within a few minutes on a typical desktop.

You can install the development version of TEMPTED from GitHub with:

# install.packages("devtools")
devtools::install_github("pixushi/tempted")

or download the tarball to your folder of interest and install using

install.packages("folder_of_interest/tempted_0.1.0.tar.gz", repos = NULL, type="source")

Load packages for this vignette

library(gridExtra)
library(tempted)

Read the example data

The example dataset is originally from Bokulich, Nicholas A., et al. (2016). We provide three data objects:

meta_table: A data.frame with rows representing samples and matching with data.frame count_table and processed_table and three columns:
- studyid: character denoting the subject ID of the infants.
- delivery: character denoting the delivery mode of the infants.}
- day_of_life: character denoting the age of infants measured in days when microbiome sample was taken.
count_tabe: A data.frame with rows representing samples and matching with data.frame meta_table and columns representing microbial features (i.e. OTUs). Each entry is a read count.
processed_table: A data.frame with rows representing samples and matching with data.frame meta_table and columns representing microbial features (i.e. ASVs, genes). Entries do not need to be transformed, and will be directly used by tempted(). This data.frame is used to illustrate how tempted() can be used for general form of multivariate longitudinal data already preprocessed by user.

# match rows of different data frames
# check number of samples
table(rownames(count_table)==rownames(meta_table))
#> 
#> TRUE 
#>  852
metauni <- unique(meta_table[,c('studyid', 'delivery')])

Running TEMPTED for different formats of data

We provide example codes for the following scenarios:

Run TEMPTED for Microbiome Count Data (Straightforward Way)
Run TEMPTED for Microbiome Compositional Data (Straightforward Way)
Run TEMPTED for General Form of Multivariate Longitudinal Data (Straightforward Way)
Run TEMPTED in Customized Way
Transferring TEMPTED result from training to testing data

Run TEMPTED for Microbiome Count Data (Straightforward Way)

Run TEMPTED

A complete description of all parameters can be found in the pdf manual. Here we explain the key parameters:

feature_table: A sample by feature matrix.
time_point: The time stamp of each sample, matched with the rows of feature_table.
subjectID: The subject ID of each sample, matched with the rows of feature_table.
threshold: A threshold for feature filtering for microbiome data. Features with zero value percentage >= threshold will be excluded. Default is 0.95.
smooth: Smoothing parameter for RKHS norm. Larger means smoother temporal loading functions. Default is set to be 1e-8. Value can be adjusted depending on the dataset by checking the smoothness of the estimated temporal loading function in plot.
transform: The transformation applied to the data. “logcomp” for log of compositions. “comp” for compositions. “ast” for arcsine squared transformation. “clr” for central log ratio transformation. “logit” for logit transformation. “lfb” for log fold over baseline. “none” for no transformation. Default transform=“clr” is recommended for microbiome data. For data that are already transformed, use transform=“none”.
r: Number of components to decompose into, i.e. rank of the CP type decomposition. Default is set to 3.
pct_ratio: The percent of features to sum up for taking log ratios. Default is 0.05, i.e. 5%.
absolute: absolute = TRUE means features are ranked by the absolute value of feature loadings, and the top pct_ratio percent of features are picked. absolute = FALSE means features are ranked by the original value of feature loadings, and the top and bottom pct_ratio percent of features are picked. Then ratio is taken as the abundance of the features with positive loading over the abundance of the features with negative loading. Input for ratio_feature.
pct_aggregate: The percent of features to aggregate, features ranked by absolute value of the feature loading of each component. Default is 1, which means 100% of features are aggregated. Setting pct_aggregate = 0.01 means top 1% of features is aggregated, where features are ranked in absolute value of feature loading of each component. Input for aggregate_feature.
pseudo: A small number to add to all the counts before normalizing into proportions and log transformation. Default is 1/2 of the smallest non-zero value that is specific for each sample. This pseudo count is added for transform=c("logcomp", "clr", "logit", "lfb").

IMPORTANT NOTE: In matrix singular value decomposition, the sign of subject scores and feature loadings can be flipped together. Similarly, you can flip the signs of any pair of subject loadings, feature loadings, and temporal loadings.

res_count <- tempted_all(count_table,
                         meta_table$day_of_life,
                         meta_table$studyid,
                         threshold=0.95,
                         transform="clr",
                         pseudo=0.5,
                         r=2,
                         smooth=1e-5,
                         pct_ratio=0.1,
                         pct_aggregate=1)
#> Calculate the 1th Component
#> Convergence reached at dif=3.57400400849311e-05, iter=4
#> Calculate the 2th Component
#> Convergence reached at dif=4.745809269163e-05, iter=7

Low-dimensional representation of subjects

Subject loadings are stored in variable A_hat of the tempted_all() output.

A_data <- metauni
rownames(A_data) <- A_data$studyid
A_data <- cbind(res_count$A_hat[rownames(A_data),], A_data)

p_subj <- ggplot(data=A_data, aes(x=A_data[,1], y=A_data[,2], color=delivery)) + 
  geom_point() +
  labs(x='Component 1', y='Component 2', title='subject loading') 
print(p_subj)

Plot the temporal loadings

Temporal loadings are stored in variable Phi_hat of the tempted_all() output. We provide an R function plot_time_loading() to plot these curves. Option r lets you decide how many components to plot.

p_time <- plot_time_loading(res_count, r=2) + 
  geom_line(size=1.5) + 
  labs(title='temporal loadings', x='days')
print(p_time)

Plot the feature loadings

Feature loadings are stored in variable B_hat of the tempted_all() output.

p_feature <- ggplot(as.data.frame(res_count$B_hat), aes(x=PC1, y=PC2)) + 
  geom_point() + 
  labs(x='Component 1', y='Component 2', title='feature loading')
print(p_feature)

Plot log ratio of top features

The log ratios are stored in variable metafeature_ratio of the tempted_all() output.

group <- unique(meta_table[,c("studyid", "delivery")])
plot_metafeature(res_count$metafeature_ratio, group) + xlab("Days of Life")
#> Multistart 1 of 1 |Multistart 1 of 1 |Multistart 1 of 1 |Multistart 1 of 1 /Multistart 1 of 1 |Multistart 1 of 1 |                   Multistart 1 of 1 |Multistart 1 of 1 |Multistart 1 of 1 |Multistart 1 of 1 /Multistart 1 of 1 |Multistart 1 of 1 |                   Multistart 1 of 1 |Multistart 1 of 1 |Multistart 1 of 1 |Multistart 1 of 1 /Multistart 1 of 1 |Multistart 1 of 1 |                   Multistart 1 of 1 |Multistart 1 of 1 |Multistart 1 of 1 |Multistart 1 of 1 /Multistart 1 of 1 |Multistart 1 of 1 |

Plot subject trajectories

The subject trajectores are stored in metafeature_aggregate of the tempted_all() output.

group <- unique(meta_table[,c("studyid", "delivery")])
plot_metafeature(res_count$metafeature_aggregate, group) + xlab("Days of Life")
#> Multistart 1 of 1 |Multistart 1 of 1 |Multistart 1 of 1 |Multistart 1 of 1 /Multistart 1 of 1 |Multistart 1 of 1 |                   Multistart 1 of 1 |Multistart 1 of 1 |Multistart 1 of 1 |Multistart 1 of 1 /Multistart 1 of 1 |Multistart 1 of 1 |                   Multistart 1 of 1 |Multistart 1 of 1 |Multistart 1 of 1 |Multistart 1 of 1 /Multistart 1 of 1 |Multistart 1 of 1 |                   Multistart 1 of 1 |Multistart 1 of 1 |Multistart 1 of 1 |Multistart 1 of 1 /Multistart 1 of 1 |Multistart 1 of 1 |

Low-dimensional representation of samples

This is an alternative way to visualize the subject trajectories. Instead of plotting against the time points, you can visualize the samples in low-dimensional spaces.

tab_feat_obs <- res_count$metafeature_aggregate
colnames(tab_feat_obs)[2] <- 'studyid'
tab_feat_obs <- merge(tab_feat_obs, metauni)

reshape_feat_obs <- reshape(tab_feat_obs, 
                            idvar=c("studyid","timepoint") , 
                            v.names=c("value"), timevar="PC",
                            direction="wide")
colnames(reshape_feat_obs) <- 
  sub(".*value[.]", "",  colnames(reshape_feat_obs))
colnames(reshape_feat_obs)
#> [1] "studyid"   "timepoint" "delivery"  "PC1"       "PC2"

p_aggfeat_scatter <- ggplot(data=reshape_feat_obs, aes(x=PC1, y=PC2, 
                             color=timepoint, shape=delivery)) +
  geom_point() + scale_color_gradient(low = "#2b83ba", high = "#d7191c") + 
  labs(x='Component 1', y='Component 2', color='Day')
p_aggfeat_scatter

# subsetting timepoint between 3 months and 1 year
p_aggfeat_scatter2 <- ggplot(data=dplyr::filter(reshape_feat_obs, timepoint<365 & timepoint>30),
                             aes(x=PC1, y=PC2, 
                             color=delivery)) +
  geom_point() + 
  labs(x='Component 1', y='Component 2', color='Delivery Mode')
p_aggfeat_scatter2

Run TEMPTED for Microbiome Compositional Data (Straightforward Way)

Run TEMPTED

IMPORTANT NOTE: Different form the count data, pseudo = NULL is used so that 1/2 of the smallest non-zero value is added to each sample. This pseudo count is added for transform=c("logcomp", "clr", "logit", "lfb").

proportion_table <- count_table/rowSums(count_table)
res_proportion <- tempted_all(proportion_table,
                              meta_table$day_of_life,
                              meta_table$studyid,
                              threshold=0.95,
                              transform="clr",
                              pseudo=NULL,
                              r=2,
                              smooth=1e-5)
#> Calculate the 1th Component
#> Convergence reached at dif=3.57400414642375e-05, iter=4
#> Calculate the 2th Component
#> Convergence reached at dif=4.7458092689688e-05, iter=7

Low-dimensional representation of subjects

A_data <- metauni
rownames(A_data) <- A_data$studyid
A_data <- cbind(res_proportion$A_hat[rownames(A_data),], A_data)

p_subj <- ggplot(data=A_data, aes(x=A_data[,1], y=A_data[,2], color=delivery)) + 
  geom_point() + 
  labs(x='Component 1', y='Component 2', title='subject loading') 
print(p_subj)

Plot the temporal loadings

p_time <- plot_time_loading(res_proportion, r=2) + 
  geom_line(size=1.5) + 
  labs(title='temporal loadings', x='days')
print(p_time)

Plot the feature loadings

pfeature <- ggplot(as.data.frame(res_proportion$B_hat), aes(x=PC1, y=PC2)) + 
  geom_point() + 
  labs(x='Component 1', y='Component 2', title='feature loading')
print(pfeature)

Plot log ratio of top features

group <- unique(meta_table[,c("studyid", "delivery")])
plot_metafeature(res_proportion$metafeature_ratio, group) + xlab("Days of Life")
#> Multistart 1 of 1 |Multistart 1 of 1 |Multistart 1 of 1 |Multistart 1 of 1 /Multistart 1 of 1 |Multistart 1 of 1 |                   Multistart 1 of 1 |Multistart 1 of 1 |Multistart 1 of 1 |Multistart 1 of 1 /Multistart 1 of 1 |Multistart 1 of 1 |                   Multistart 1 of 1 |Multistart 1 of 1 |Multistart 1 of 1 |Multistart 1 of 1 /Multistart 1 of 1 |Multistart 1 of 1 |                   Multistart 1 of 1 |Multistart 1 of 1 |Multistart 1 of 1 |Multistart 1 of 1 /Multistart 1 of 1 |Multistart 1 of 1 |

Plot subject trajectories

group <- unique(meta_table[,c("studyid", "delivery")])
plot_metafeature(res_proportion$metafeature_aggregate, group) + xlab("Days of Life")
#> Multistart 1 of 1 |Multistart 1 of 1 |Multistart 1 of 1 |Multistart 1 of 1 /Multistart 1 of 1 |Multistart 1 of 1 |                   Multistart 1 of 1 |Multistart 1 of 1 |Multistart 1 of 1 |Multistart 1 of 1 /Multistart 1 of 1 |Multistart 1 of 1 |                   Multistart 1 of 1 |Multistart 1 of 1 |Multistart 1 of 1 |Multistart 1 of 1 /Multistart 1 of 1 |Multistart 1 of 1 |                   Multistart 1 of 1 |Multistart 1 of 1 |Multistart 1 of 1 |Multistart 1 of 1 /Multistart 1 of 1 |Multistart 1 of 1 |

Low-dimensional representation of samples

This is an alternative way to visualize the subject trajectories. Instead of plotting against the time points, you can visualize the samples in low-dimensional spaces.

tab_feat_obs <- res_proportion$metafeature_aggregate
colnames(tab_feat_obs)[2] <- 'studyid'
tab_feat_obs <- merge(tab_feat_obs, metauni)

reshape_feat_obs <- reshape(tab_feat_obs, 
                            idvar=c("studyid","timepoint") , 
                            v.names=c("value"), timevar="PC",
                            direction="wide")
colnames(reshape_feat_obs) <- 
  sub(".*value[.]", "",  colnames(reshape_feat_obs))
colnames(reshape_feat_obs)
#> [1] "studyid"   "timepoint" "delivery"  "PC1"       "PC2"

p_aggfeat_scatter <- ggplot(data=reshape_feat_obs, aes(x=PC1, y=PC2, 
                             color=timepoint, shape=delivery)) +
  geom_point() + scale_color_gradient(low = "#2b83ba", high = "#d7191c") + 
  labs(x='Component 1', y='Component 2', color='Day')
p_aggfeat_scatter

# subsetting timepoint between 3 months and 1 year
p_aggfeat_scatter2 <- ggplot(data=dplyr::filter(reshape_feat_obs, timepoint<365 & timepoint>30),
                             aes(x=PC1, y=PC2, 
                             color=delivery)) +
  geom_point() + 
  labs(x='Component 1', y='Component 2', color='Delivery Mode')
p_aggfeat_scatter2

Run TEMPTED for General Form of Multivariate Longitudinal Data (Straightforward Way)

Run TEMPTED

IMPORTANT NOTE: Different form the microbiome data, no features are going to be filtered out by setting threshold=1, no transformation is performed by setting transform="none", and no log ratio is calculated by setting do_ratio=FALSE.

res_processed <- tempted_all(processed_table,
                             meta_table$day_of_life,
                             meta_table$studyid,
                             threshold=1,
                             transform="none",
                             r=2,
                             smooth=1e-5,
                             do_ratio=FALSE)
#> Calculate the 1th Component
#> Convergence reached at dif=3.8157412154411e-05, iter=4
#> Calculate the 2th Component
#> Convergence reached at dif=2.44419512850139e-05, iter=7

Low-dimensional representation of subjects

A_data <- metauni
rownames(A_data) <- A_data$studyid
A_data <- cbind(res_processed$A_hat[rownames(A_data),], A_data)

p_subj <- ggplot(data=A_data, aes(x=A_data[,1], y=A_data[,2], color=delivery)) + 
  geom_point() + 
  labs(x='Component 1', y='Component 2', title='subject loading') 
print(p_subj)

Plot the temporal loadings

p_time <- plot_time_loading(res_processed, r=2) + 
  geom_line(size=1.5) + 
  labs(title='temporal loadings', x='days')
print(p_time)

Plot the feature loadings

pfeature <- ggplot(as.data.frame(res_processed$B_hat), aes(x=PC1, y=PC2)) + 
  geom_point() + 
  labs(x='Component 1', y='Component 2', title='feature loading')
print(pfeature)

Plot subject trajectories

group <- unique(meta_table[,c("studyid", "delivery")])
plot_metafeature(res_processed$metafeature_aggregate, group) + xlab("Days of Life")
#> Multistart 1 of 1 |Multistart 1 of 1 |Multistart 1 of 1 |Multistart 1 of 1 /Multistart 1 of 1 |Multistart 1 of 1 |                   Multistart 1 of 1 |Multistart 1 of 1 |Multistart 1 of 1 |Multistart 1 of 1 /Multistart 1 of 1 |Multistart 1 of 1 |                   Multistart 1 of 1 |Multistart 1 of 1 |Multistart 1 of 1 |Multistart 1 of 1 /Multistart 1 of 1 |Multistart 1 of 1 |                   Multistart 1 of 1 |Multistart 1 of 1 |Multistart 1 of 1 |Multistart 1 of 1 /Multistart 1 of 1 |Multistart 1 of 1 |

Low-dimensional representation of samples

tab_feat_obs <- res_processed$metafeature_aggregate
colnames(tab_feat_obs)[2] <- 'studyid'
tab_feat_obs <- merge(tab_feat_obs, metauni)

reshape_feat_obs <- reshape(tab_feat_obs, 
                            idvar=c("studyid","timepoint") , 
                            v.names=c("value"), timevar="PC",
                            direction="wide")
colnames(reshape_feat_obs) <- 
  sub(".*value[.]", "",  colnames(reshape_feat_obs))
colnames(reshape_feat_obs)
#> [1] "studyid"   "timepoint" "delivery"  "PC1"       "PC2"

p_aggfeat_scatter <- ggplot(data=reshape_feat_obs, aes(x=PC1, y=PC2, 
                             color=timepoint, shape=delivery)) +
  geom_point() + scale_color_gradient(low = "#2b83ba", high = "#d7191c") + 
  labs(x='Component 1', y='Component 2', color='Day')
p_aggfeat_scatter

# subsetting timepoint between 3 months and 1 year
p_aggfeat_scatter2 <- ggplot(data=dplyr::filter(reshape_feat_obs, timepoint<365 & timepoint>30),
                             aes(x=PC1, y=PC2, 
                             color=delivery)) +
  geom_point() + 
  labs(x='Component 1', y='Component 2', color='Delivery Mode')
p_aggfeat_scatter2

Run TEMPTED in Customized Way

This is a breakdown of what tempted_all() does in each function it wraps into.

Format and Transform Data

The function format_tempted() transforms the sample-by-feature table and the corresponding time points and subject IDs into the list format that is accepted by tempted(). It filters features with a lot of zeros, perform transformation of the features, and add pseudo count for transformations that cannot handle zeros. When a subject has multiple samples from the same time point, format_tempted() will only keep the first sample in the data input.

IMPORTANT NOTE: For read count table as feature_table, set pseudo=0.5. For compositional/proportion data as feature_table, default setting is appropriate. For non-microbiome data, set transform="none" and threshold=1.

# format the data frames into a list that can be used by TEMPTED
datlist <- format_tempted(count_table, meta_table$day_of_life, meta_table$studyid, threshold=0.95, pseudo=0.5, transform="clr")
length(datlist)
#> [1] 42
print(dim(datlist[[1]]))
#> [1] 796  29

Run TEMPTED

The function svd_centralize() uses matrix SVD to fit a constant trajectory (straight flat line) for all subject-feature pairs, and remove it from the data. This step is optional. If it is not used, we recommend the user to add 1 to the rank parameter r in tempted() and in general the first component estimated by tempted() will reflect this constant trajectory. In this example, we used r=2. Option smooth allows the user to choose the smoothness of the estimated temporal loading.

# centralize data using matrix SVD after log 
svd_tempted <- svd_centralize(datlist)
res_tempted <- tempted(svd_tempted$datlist, r = 2, resolution = 101, smooth=1e-5)
#> Calculate the 1th Component
#> Convergence reached at dif=3.531461408802e-05, iter=4
#> Calculate the 2th Component
#> Convergence reached at dif=4.37783267396658e-05, iter=7
# alternatively, you can replace the two lines above by the two lines below.
# the 2nd and 3rd component in the result below will be 
# similar to the 1st and 2nd component in the result above.
#svd_tempted <- NULL
#res_tempted <- tempted(datlist, r = 3, resolution = 101)

The output of tempted() can be used in the same way as the output of tempted_all() to plot temporal loadings, subject loadings, and feature loadings as in the previous sections of this document.

Log ratio of top/bottom feature

The feature loadings can be used to rank features. The abundance ratio of top ranking features over bottom ranking features corresponding to each component can be a biologically meaningful marker. We provide an R function ratio_feature() to calculate such the abundance ratio. The abundance ratio is stored in the output variable metafeature_ratio in the output. An TRUE/FALSE vector indicating whether the feature is in the top ranking or bottom ranking is stored in variable toppct and bottompct, respectively. Below are trajectories of the aggregated features using observed data. Users can choose the percentage for the cutoff of top/bottom ranking features through option pct (by default pct=0.05). By default absolute=TRUE means the features are chosen if they rank in the top pct percentile in the absolute value of the feature loadings, and abundance ratio is taken between the features with positive loadings over negative loadings. When absolute=FALSE, the features are chose if they rank in the top pct percentile and has positive loading or rank in the bottom pct percentile and has negative loading. We also provide an option contrast allowing users to rank features using linear combinations of the feature loadings from different components.

datlist_raw <- format_tempted(count_table, meta_table$day_of_life, meta_table$studyid, 
                            threshold=0.95, transform='none')
contrast <- cbind(c(1/2,1), c(1/2,-1))
contrast
#>      [,1] [,2]
#> [1,]  0.5  0.5
#> [2,]  1.0 -1.0

ratio_feat <- ratio_feature(res_tempted, datlist_raw,
                        contrast=contrast, pct=0.1)
tab_feat_obs <- ratio_feat$metafeature_ratio
colnames(tab_feat_obs)[2] <- 'studyid'
tab_feat_obs <- merge(tab_feat_obs, metauni)
colnames(tab_feat_obs)
#> [1] "studyid"   "value"     "timepoint" "PC"        "delivery"
p_feat_obs <- ggplot(data=tab_feat_obs, 
                      aes(x=timepoint, y=value, group=studyid, color=delivery)) +
  geom_line() + facet_wrap(.~PC, scales="free", nrow=1) + xlab("Days of Life")

p_feat_obs_summary <- plot_metafeature(ratio_feat$metafeature_ratio, group, bws=30, nrow=1) + xlab("Days of Life")

grid.arrange(p_feat_obs, p_feat_obs_summary, nrow=2)

Subject trajectories

The feature loadings can be used as weights to aggregate features. The aggregation can be done using the low-rank denoised data tensor, or the original observed data tensor. We provide an R function aggregate_feature() to perform the aggregation. The aggregated features using low-rank denoised tensor is stored in variable metafeature_aggregate_est and the aggregated features using observed data is stored in variable metafeature_aggregate. Below are trajectories of the aggregated features using observed data. Only the features with absolute loading in the top pct percentile (by default set to 100%, i.e. all features, through option pct=1) are used for the aggregation. We also provide an option contrast allowing users to aggregate features using linear combinations of the feature loadings from different components.

## observed, by individual subject
contrast <- cbind(c(1/2,1), c(1/2,-1))
agg_feat <- aggregate_feature(res_tempted, svd_tempted, datlist, 
                              contrast=contrast, pct=1)
tab_feat_obs <- agg_feat$metafeature_aggregate
colnames(tab_feat_obs)[2] <- 'studyid'
tab_feat_obs <- merge(tab_feat_obs, metauni)
colnames(tab_feat_obs)
#> [1] "studyid"   "value"     "timepoint" "PC"        "delivery"
p_feat_obs <- ggplot(data=tab_feat_obs, 
                      aes(x=timepoint, y=value, group=studyid, color=delivery)) +
  geom_line() + facet_wrap(.~PC, scales="free", nrow=1) + xlab("Days of Life")

p_feat_obs_summary <- plot_metafeature(agg_feat$metafeature_aggregate, group, bws=30, nrow=1) + xlab("Days of Life")

grid.arrange(p_feat_obs, p_feat_obs_summary, nrow=2)

Plot trajectory of top features

The feature loadings can also be used to investigate the driving features behind each component. Here we focus on the 2nd component and provide the trajectories of the top features using the estimated and observed data tensor, respectively.

proportion_table <- count_table/rowSums(count_table)
feat_names <- c("OTU4447072", "OTU4467447")
# individual samples
tab_sel_feat <- cbind(proportion_table[,feat_names], meta_table)
tab_sel_feat <- reshape(tab_sel_feat, 
                        varying=list(feat_names), 
                        times=feat_names, 
                        timevar="feature", 
                        v.names="RA", 
                        ids=rownames(tab_sel_feat),
                        direction="long")
p_topfeat <- ggplot(data=tab_sel_feat) + 
  geom_point(aes(x=day_of_life, y=RA, color=delivery)) +
  facet_wrap(vars(feature)) + 
  labs(x="Day of Life", y="Relative Abundance") + 
  coord_trans(y="sqrt")
# summary plot
p_topfeat_summary <- plot_feature_summary(proportion_table[,feat_names], 
                     meta_table$day_of_life, 
                     meta_table$delivery, 
                     bws=30) + 
  labs(x="Day of Life", y="Relative Abundance")
grid.arrange(p_topfeat, p_topfeat_summary, nrow=2)

Transferring TEMPTED result from training to testing data

Split the example data into training and testing

Here we take thes subject with studyid="2" as the testing subject, and the remaining subjects as training subjects.

id_test <- meta_table$studyid=="2"

count_train <- count_table[!id_test,]
meta_train <- meta_table[!id_test,]

count_test <- count_table[id_test,]
meta_test <- meta_table[id_test,]

Run TEMPTED on training subjects

datlist_train <- format_tempted(count_train,
                                meta_train$day_of_life,
                                meta_train$studyid,
                                threshold=0.95,
                                pseudo=0.5,
                                transform="clr")

mean_svd_train <- svd_centralize(datlist_train, r=1)

res_tempted_train <- tempted(mean_svd_train$datlist,
r=2, smooth=1e-5)
#> Calculate the 1th Component
#> Convergence reached at dif=3.89952383939211e-05, iter=4
#> Calculate the 2th Component
#> Convergence reached at dif=4.45458808530784e-05, iter=7

Obtain subject loading for testing subject

IMPORTANT NOTE: the testing samples should contain the features in the training data.

# get the overlapping features between testing and training
count_test <- count_test[,rownames(datlist_train[[1]])[-1]]

# format testing data
datlist_test <- format_tempted(count_test,
                               meta_test$day_of_life,
                               meta_test$studyid,
                               threshold=1,
                               pseudo=0.5,
                               transform="clr")

# estimate the subject loading of the testing subject
sub_test <- est_test_subject(datlist_test, res_tempted_train, mean_svd_train)
sub_test
#>           PC1       PC2
#> 2 -0.07967744 0.1688863

Here we use logistic regression to illustrate how the subject loadings of the testing data can be used.

# train logistic regression classifier on training subjects
metauni <- unique(meta_table[,c("studyid", "delivery")])
rownames(metauni) <- metauni$studyid
Atrain <- as.data.frame(res_tempted_train$A_hat)
Atrain$delivery <- metauni[rownames(Atrain),"delivery"]=="Cesarean"
glm_train <- glm(delivery ~ PC1+PC2,
                 data=Atrain, family=binomial(link="logit"))
summary(glm_train)
#> 
#> Call:
#> glm(formula = delivery ~ PC1 + PC2, family = binomial(link = "logit"), 
#>     data = Atrain)
#> 
#> Coefficients:
#>             Estimate Std. Error z value Pr(>|z|)   
#> (Intercept)   -2.965      1.652  -1.795  0.07266 . 
#> PC1          -11.334      9.129  -1.242  0.21440   
#> PC2           16.865      5.529   3.050  0.00229 **
#> ---
#> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
#> 
#> (Dispersion parameter for binomial family taken to be 1)
#> 
#>     Null deviance: 55.637  on 40  degrees of freedom
#> Residual deviance: 34.562  on 38  degrees of freedom
#> AIC: 40.562
#> 
#> Number of Fisher Scoring iterations: 6

# predict the label of testing subject "2", whose true label is "Cesarean"
predict(glm_train, newdata=as.data.frame(sub_test), type="response")
#>         2 
#> 0.6870014

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data		data
inst		inst
man		man
DESCRIPTION		DESCRIPTION
Fig_tempted.png		Fig_tempted.png
NAMESPACE		NAMESPACE
README.Rmd		README.Rmd
README.md		README.md
tempted_0.1.0.pdf		tempted_0.1.0.pdf
tempted_0.1.0.tar.gz		tempted_0.1.0.tar.gz
tempted_0.1.1.pdf		tempted_0.1.1.pdf
tempted_0.1.1.tar.gz		tempted_0.1.1.tar.gz

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TEMPTED Vignette

Introduction of TEMPTED

Installation

Load packages for this vignette

Read the example data

Running TEMPTED for different formats of data

Run TEMPTED for Microbiome Count Data (Straightforward Way)

Run TEMPTED

Low-dimensional representation of subjects

Plot the temporal loadings

Plot the feature loadings

Plot log ratio of top features

Plot subject trajectories

Low-dimensional representation of samples

Run TEMPTED for Microbiome Compositional Data (Straightforward Way)

Run TEMPTED

Low-dimensional representation of subjects

Plot the temporal loadings

Plot the feature loadings

Plot log ratio of top features

Plot subject trajectories

Low-dimensional representation of samples

Run TEMPTED for General Form of Multivariate Longitudinal Data (Straightforward Way)

Run TEMPTED

Low-dimensional representation of subjects

Plot the temporal loadings

Plot the feature loadings

Plot subject trajectories

Low-dimensional representation of samples

Run TEMPTED in Customized Way

Format and Transform Data

Run TEMPTED

Log ratio of top/bottom feature

Subject trajectories

Plot trajectory of top features

Transferring TEMPTED result from training to testing data

Split the example data into training and testing

Run TEMPTED on training subjects

Obtain subject loading for testing subject

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