| Title: | Infer Copy Number Variation from Single-Cell RNA-Seq Data |
|---|---|
| Description: | Using single-cell RNA-Seq expression to visualize CNV in cells. |
| Authors: | Timothy Tickle [aut], Itay Tirosh [aut], Christophe Georgescu [aut, cre], Maxwell Brown [aut], Brian Haas [aut] |
| Maintainer: | Christophe Georgescu <[email protected]> |
| License: | BSD_3_clause + file LICENSE |
| Version: | 1.23.0 |
| Built: | 2024-10-30 08:35:17 UTC |
| Source: | https://github.com/bioc/infercnv |
Using single-cell RNA-Seq expression to visualize CNV in cells.
The main functions you will need to use are CreateInfercnvObject() and run(infercnv_object). For additional details on running the analysis step by step, please refer to the example vignette.
Maintainer: Christophe Georgescu [email protected]
Authors:
Timothy Tickle [email protected]
Itay Tirosh [email protected]
Maxwell Brown [email protected]
Brian Haas [email protected]
Useful links:
Report bugs at https://github.com/broadinstitute/inferCNV/issues
Add meta.data about CNAs to a Seurat object from an infercnv_obj
add_to_seurat( seurat_obj = NULL, assay_name = "RNA", infercnv_output_path, top_n = 10, bp_tolerance = 2e+06, column_prefix = NULL )add_to_seurat( seurat_obj = NULL, assay_name = "RNA", infercnv_output_path, top_n = 10, bp_tolerance = 2e+06, column_prefix = NULL )
seurat_obj |
Seurat object to add meta.data to (default: NULL) |
assay_name |
Name of the assay in the Seurat object if provided. (default: "RNA") |
infercnv_output_path |
Path to the output folder of the infercnv run to use |
top_n |
How many of the largest CNA (in number of genes) to get. |
bp_tolerance |
How many bp of tolerance to have around feature start/end positions for top_n largest CNVs. |
column_prefix |
String to add as a prefix to the Seurat metadata columns. Only applied to the seurat_obj, if supplied. Default is NULL |
seurat_obj
Apply a median filtering to the expression matrix within each tumor bounds
apply_median_filtering( infercnv_obj, window_size = 7, on_observations = TRUE, on_references = TRUE )apply_median_filtering( infercnv_obj, window_size = 7, on_observations = TRUE, on_references = TRUE )
infercnv_obj |
infercnv_object |
window_size |
Size of the window side centered on the data point to filter (default = 7). |
on_observations |
boolean (default=TRUE), run on observations data (tumor cells). |
on_references |
boolean (default=TRUE), run on references (normal cells). |
infercnv_obj with median filtering applied to observations
# data(infercnv_data_example) # data(infercnv_annots_example) # data(infercnv_genes_example) # infercnv_object_example <- infercnv::CreateInfercnvObject(raw_counts_matrix=infercnv_data_example, # gene_order_file=infercnv_genes_example, # annotations_file=infercnv_annots_example, # ref_group_names=c("normal")) # infercnv_object_example <- infercnv::run(infercnv_object_example, # cutoff=1, # out_dir=tempfile(), # cluster_by_groups=TRUE, # denoise=TRUE, # HMM=FALSE, # num_threads=2, # no_plot=TRUE) data(infercnv_object_example) infercnv_object_example <- infercnv::apply_median_filtering(infercnv_object_example) # plot result object# data(infercnv_data_example) # data(infercnv_annots_example) # data(infercnv_genes_example) # infercnv_object_example <- infercnv::CreateInfercnvObject(raw_counts_matrix=infercnv_data_example, # gene_order_file=infercnv_genes_example, # annotations_file=infercnv_annots_example, # ref_group_names=c("normal")) # infercnv_object_example <- infercnv::run(infercnv_object_example, # cutoff=1, # out_dir=tempfile(), # cluster_by_groups=TRUE, # denoise=TRUE, # HMM=FALSE, # num_threads=2, # no_plot=TRUE) data(infercnv_object_example) infercnv_object_example <- infercnv::apply_median_filtering(infercnv_object_example) # plot result object
Helper function allowing greater control over the steps in a color palette. Source: http://menugget.blogspot.com/2011/11/define-color-steps-for- colorramppalette.html#more
color.palette(steps, between = NULL, ...)color.palette(steps, between = NULL, ...)
steps |
Vector of colors to change use in the palette |
between |
Steps where gradients change |
... |
Additional arguments of colorRampPalette |
Color palette
color.palette(c("darkblue", "white", "darkred"), c(2, 2))color.palette(c("darkblue", "white", "darkred"), c(2, 2))
Creation of an infercnv object. This requires the following inputs: A more detailed description of each input is provided below:
The raw_counts_matrix:
MGH54_P16_F12 MGH53_P5_C12 MGH54_P12_C10 MGH54_P16_F02 MGH54_P11_C11 ... DDX11L1 0.0000000 0.000000 0.000000 0.000000 0.0000000 WASH7P 0.0000000 2.231939 7.186235 5.284944 0.9650009 FAM138A 0.1709991 0.000000 0.000000 0.000000 0.0000000 OR4F5 0.0000000 0.000000 0.000000 0.000000 0.0000000 OR4F29 0.0000000 0.000000 0.000000 0.000000 0.0000000 ...
The gene_order_file, contains chromosome, start, and stop position for each gene, tab-delimited:
chr start stop DDX11L1 chr1 11869 14412 WASH7P chr1 14363 29806 FAM138A chr1 34554 36081 OR4F5 chr1 69091 70008 OR4F29 chr1 367640 368634 OR4F16 chr1 621059 622053 ...
The annotations_file, containing the cell name and the cell type classification, tab-delimited.
V1 V2 1 MGH54_P2_C12 Microglia/Macrophage 2 MGH36_P6_F03 Microglia/Macrophage 3 MGH53_P4_H08 Microglia/Macrophage 4 MGH53_P2_E09 Microglia/Macrophage 5 MGH36_P5_E12 Oligodendrocytes (non-malignant) 6 MGH54_P2_H07 Oligodendrocytes (non-malignant) ... 179 93_P9_H03 malignant 180 93_P10_D04 malignant 181 93_P8_G09 malignant 182 93_P10_B10 malignant 183 93_P9_C07 malignant 184 93_P8_A12 malignant ...
and the ref_group_names vector might look like so: c("Microglia/Macrophage","Oligodendrocytes (non-malignant)")
CreateInfercnvObject( raw_counts_matrix, gene_order_file, annotations_file, ref_group_names, delim = "\t", max_cells_per_group = NULL, min_max_counts_per_cell = c(100, +Inf), chr_exclude = c("chrX", "chrY", "chrM") )CreateInfercnvObject( raw_counts_matrix, gene_order_file, annotations_file, ref_group_names, delim = "\t", max_cells_per_group = NULL, min_max_counts_per_cell = c(100, +Inf), chr_exclude = c("chrX", "chrY", "chrM") )
raw_counts_matrix |
the matrix of genes (rows) vs. cells (columns) containing the raw counts If a filename is given, it'll be read via read.table() otherwise, if matrix or Matrix, will use the data directly. |
gene_order_file |
data file containing the positions of each gene along each chromosome in the genome. |
annotations_file |
a description of the cells, indicating the cell type classifications |
ref_group_names |
a vector containing the classifications of the reference (normal) cells to use for infering cnv |
delim |
delimiter used in the input files |
max_cells_per_group |
maximun number of cells to use per group. Default=NULL, using all cells defined in the annotations_file. This option is useful for randomly subsetting the existing data for a quicker preview run, such as using 50 cells per group instead of hundreds. |
min_max_counts_per_cell |
minimum and maximum counts allowed per cell. Any cells outside this range will be removed from the counts matrix. default=(100, +Inf) and uses all cells. If used, should be set as c(min_counts, max_counts) |
chr_exclude |
list of chromosomes in the reference genome annotations that should be excluded from analysis. Default = c('chrX', 'chrY', 'chrM') |
infercnv
data(infercnv_data_example) data(infercnv_annots_example) data(infercnv_genes_example) infercnv_object_example <- infercnv::CreateInfercnvObject(raw_counts_matrix=infercnv_data_example, gene_order_file=infercnv_genes_example, annotations_file=infercnv_annots_example, ref_group_names=c("normal"))data(infercnv_data_example) data(infercnv_annots_example) data(infercnv_genes_example) infercnv_object_example <- infercnv::CreateInfercnvObject(raw_counts_matrix=infercnv_data_example, gene_order_file=infercnv_genes_example, annotations_file=infercnv_annots_example, ref_group_names=c("normal"))
The following function will filter the HMM identified CNV's by the CNV's posterior probability of belonging to a normal state identified by the function inferCNVBayesNet(). Will filter CNV's based on a user desired threshold probability. Any CNV with a probability of being normal above the threshold will be removed.
filterHighPNormals(MCMC_inferCNV_obj, HMM_states, BayesMaxPNormal, useRaster)filterHighPNormals(MCMC_inferCNV_obj, HMM_states, BayesMaxPNormal, useRaster)
MCMC_inferCNV_obj |
MCMC infernCNV object. |
HMM_states |
InferCNV object with HMM states in expression data. |
BayesMaxPNormal |
Option to filter CNV or cell lines by some probability threshold. |
useRaster |
Option to use rasterization when plotting |
Returns a list of (MCMC_inferCNV_obj, HMM_states) With removed CNV's.
data(mcmc_obj) mcmc_obj_hmm_states_list <- infercnv::filterHighPNormals( MCMC_inferCNV_obj = mcmc_obj, HMM_states = HMM_states, BayesMaxPNormal = 0.5)data(mcmc_obj) mcmc_obj_hmm_states_list <- infercnv::filterHighPNormals( MCMC_inferCNV_obj = mcmc_obj, HMM_states = HMM_states, BayesMaxPNormal = 0.5)
infercnv object result of the processing of run() in the HMM example, to be used for other examples.
HMM_statesHMM_states
An infercnv object containing HMM predictions
Generated classification for 10 normal cells and 10 tumor cells.
infercnv_annots_exampleinfercnv_annots_example
A data frame with 20 rows (cells) and 1 columns (classification)
Generated SmartSeq2 expression data with 10 normal cells and 10 tumor cells. This is only to demonstrate how to use methods, not actual data to be used in an analysis.
infercnv_data_exampleinfercnv_data_example
A data frame with 8252 rows (genes) and 20 columns (cells)
Downsampled gene coordinates file from GrCh37
infercnv_genes_exampleinfercnv_genes_example
A data frame with 10338 rows (genes) and 3 columns (chr, start, end)
infercnv object result of the processing of run() in the example, to be used for other examples.
infercnv_object_exampleinfercnv_object_example
An infercnv object
An infercnv object encapsulates the expression data and gene chromosome ordering information that is leveraged by infercnv for data exploration. The infercnv object is passed among the infercnv data processing and plotting routines.
Slots in the infercnv object include:
expr.data<matrix> the count or expression data matrix, manipulated throughout infercnv ops
count.data<matrix> retains the original count data, but shrinks along with expr.data when genes are removed.
gene_order<data.frame> chromosomal gene order
reference_grouped_cell_indices<list> mapping [['group_name']] to c(cell column indices) for reference (normal) cells
observation_grouped_cell_indices<list> mapping [['group_name']] to c(cell column indices) for observation (tumor) cells
tumor_subclusters<list> stores subclustering of tumors if requested
options<list> stores the options relevant to the analysis in itself (in contrast with options relevant to plotting or paths)
.hspikea hidden infercnv object populated with simulated spiked-in data
Uses Markov Chain Monte Carlo (MCMC) and Gibbs sampling to estimate the posterior probability of being in one of six Copy Number Variation states (states: 0, 0.5, 1, 1.5, 2, 3) for CNV's identified by inferCNV's HMM. Posterior probabilities are found for the entire CNV cluster and each individual cell line in the CNV.
inferCNVBayesNet( file_dir, infercnv_obj, HMM_states, out_dir, resume_file_token, model_file = NULL, CORES = 1, postMcmcMethod = NULL, plotingProbs = TRUE, quietly = TRUE, diagnostics = FALSE, HMM_type = HMM_type, k_obs_groups = k_obs_groups, cluster_by_groups = cluster_by_groups, reassignCNVs = TRUE, no_plot = no_plot, useRaster )inferCNVBayesNet( file_dir, infercnv_obj, HMM_states, out_dir, resume_file_token, model_file = NULL, CORES = 1, postMcmcMethod = NULL, plotingProbs = TRUE, quietly = TRUE, diagnostics = FALSE, HMM_type = HMM_type, k_obs_groups = k_obs_groups, cluster_by_groups = cluster_by_groups, reassignCNVs = TRUE, no_plot = no_plot, useRaster )
file_dir |
Location of the directory of the inferCNV outputs. |
infercnv_obj |
InferCNV object. |
HMM_states |
InferCNV object with HMM states in expression data. |
out_dir |
(string) Path to where the output file should be saved to. |
resume_file_token |
(string) String token that contains some info on settings used to name files. |
model_file |
Path to the BUGS Model file. |
CORES |
Option to run parallel by specifying the number of cores to be used. (Default: 1) |
postMcmcMethod |
What actions to take after finishing the MCMC. |
plotingProbs |
Option for adding plots of Cell and CNV probabilities. (Default: TRUE) |
quietly |
Option to print descriptions along each step. (Default: TRUE) |
diagnostics |
Option to plot Diagnostic plots and tables. (Default: FALSE) |
HMM_type |
The type of HMM that was ra, either 'i3' or 'i6'. Determines how many state were predicted by the HMM. |
k_obs_groups |
Number of groups in which to break the observations. (default: 1) |
cluster_by_groups |
If observations are defined according to groups (ie. patients), each group of cells will be clustered separately. (default=FALSE, instead will use k_obs_groups setting) |
reassignCNVs |
(boolean) Given the CNV associated probability of belonging to each possible state, reassign the state assignments made by the HMM to the state that has the highest probability. (default: TRUE) |
no_plot |
(boolean) Option set by infercnv::run() for producing visualizations. |
useRaster |
Option to use rasterization when plotting |
Returns a MCMC_inferCNV_obj and posterior probability of being in one of six Copy Number Variation states (states: 0, 0.5, 1, 1.5, 2, 3) for CNV's identified by inferCNV's HMM.
data(infercnv_data_example) data(infercnv_annots_example) data(infercnv_genes_example) data(HMM_states) infercnv_object_example <- infercnv::CreateInfercnvObject(raw_counts_matrix=infercnv_data_example, gene_order_file=infercnv_genes_example, annotations_file=infercnv_annots_example, ref_group_names=c("normal")) out_dir = tempfile() infercnv_object_example <- infercnv::run(infercnv_object_example, cutoff=1, out_dir=out_dir, cluster_by_groups=TRUE, analysis_mode="samples", denoise=TRUE, HMM=TRUE, num_threads=2, no_plot=TRUE) mcmc_obj <- infercnv::inferCNVBayesNet(infercnv_obj = infercnv_object_example, HMM_states = HMM_states, file_dir = out_dir, postMcmcMethod = "removeCNV", out_dir = out_dir, resume_file_token = "HMMi6.hmm_mode-samples", quietly = TRUE, CORES = 2, plotingProbs = FALSE, diagnostics = FALSE, HMM_type = 'i6', k_obs_groups = 1, cluster_by_groups = FALSE, reassignCNVs = FALSE, no_plot = TRUE)data(infercnv_data_example) data(infercnv_annots_example) data(infercnv_genes_example) data(HMM_states) infercnv_object_example <- infercnv::CreateInfercnvObject(raw_counts_matrix=infercnv_data_example, gene_order_file=infercnv_genes_example, annotations_file=infercnv_annots_example, ref_group_names=c("normal")) out_dir = tempfile() infercnv_object_example <- infercnv::run(infercnv_object_example, cutoff=1, out_dir=out_dir, cluster_by_groups=TRUE, analysis_mode="samples", denoise=TRUE, HMM=TRUE, num_threads=2, no_plot=TRUE) mcmc_obj <- infercnv::inferCNVBayesNet(infercnv_obj = infercnv_object_example, HMM_states = HMM_states, file_dir = out_dir, postMcmcMethod = "removeCNV", out_dir = out_dir, resume_file_token = "HMMi6.hmm_mode-samples", quietly = TRUE, CORES = 2, plotingProbs = FALSE, diagnostics = FALSE, HMM_type = 'i6', k_obs_groups = 1, cluster_by_groups = FALSE, reassignCNVs = FALSE, no_plot = TRUE)
Uses Markov Chain Monte Carlo (MCMC) and Gibbs sampling to estimate the posterior probability of being in one of six Copy Number Variation states (states: 0, 0.5, 1, 1.5, 2, 3) for CNV's identified by inferCNV's HMM. Posterior probabilities are found for the entire CNV cluster and each individual cell line in the CNV.
bugs_modelBUGS model.
sigfitted values for cell lines, 1/standard deviation to be used for determining the distribution of each cell line
muMean values to be used for determining the distribution of each cell line
group_idID's given to the cell clusters.
cell_geneList containing the Cells and Genes that make up each CNV.
cnv_probabilitiesProbabilities of each CNV belonging to a particular state from 0 (least likely)to 1 (most likely).
cell_probabilitiesProbabilities of each cell being in a particular state, from 0 (least likely)to 1 (most likely).
argsInput arguments given by the user
cnv_regionsID for each CNV found by the HMM
infercnv object result of the processing of inferCNVBayesNet in the example, to be used for other examples.
mcmc_objmcmc_obj
An infercnv object containing posterior probability of CNV states
Formats the data and sends it for plotting.
plot_cnv( infercnv_obj, out_dir = ".", title = "inferCNV", obs_title = "Observations (Cells)", ref_title = "References (Cells)", cluster_by_groups = TRUE, cluster_references = TRUE, plot_chr_scale = FALSE, chr_lengths = NULL, k_obs_groups = 1, contig_cex = 1, x.center = mean([email protected]), x.range = "auto", hclust_method = "ward.D", custom_color_pal = NULL, color_safe_pal = FALSE, output_filename = "infercnv", output_format = "png", png_res = 300, dynamic_resize = 0, ref_contig = NULL, write_expr_matrix = FALSE, write_phylo = FALSE, useRaster = TRUE )plot_cnv( infercnv_obj, out_dir = ".", title = "inferCNV", obs_title = "Observations (Cells)", ref_title = "References (Cells)", cluster_by_groups = TRUE, cluster_references = TRUE, plot_chr_scale = FALSE, chr_lengths = NULL, k_obs_groups = 1, contig_cex = 1, x.center = mean(infercnv_obj@expr.data), x.range = "auto", hclust_method = "ward.D", custom_color_pal = NULL, color_safe_pal = FALSE, output_filename = "infercnv", output_format = "png", png_res = 300, dynamic_resize = 0, ref_contig = NULL, write_expr_matrix = FALSE, write_phylo = FALSE, useRaster = TRUE )
infercnv_obj |
infercnv object |
out_dir |
Directory in which to save pdf and other output. |
title |
Plot title. |
obs_title |
Title for the observations matrix. |
ref_title |
Title for the reference matrix. |
cluster_by_groups |
Whether to cluster observations by their annotations or not. Using this ignores k_obs_groups. |
cluster_references |
Whether to cluster references within their annotations or not. (dendrogram not displayed) |
plot_chr_scale |
Whether to scale the chromosme width on the heatmap based on their actual size rather than just the number of expressed genes. |
chr_lengths |
A named list of chromsomes lengths to use when plot_chr_scale=TRUE, or else chromosome size is assumed to be the last chromosome's stop position + 10k bp |
k_obs_groups |
Number of groups to break observation into. |
contig_cex |
Contig text size. |
x.center |
Value on which to center expression. |
x.range |
vector containing the extreme values in the heatmap (ie. c(-3,4) ) |
hclust_method |
Clustering method to use for hclust. |
custom_color_pal |
Specify a custom set of colors for the heatmap. Has to be in the shape color.palette(c("darkblue", "white", "darkred"), c(2, 2)) |
color_safe_pal |
Logical indication of using a color blindness safe palette. |
output_filename |
Filename to save the figure to. |
output_format |
format for heatmap image file (default: 'png'), options('png', 'pdf', NA) If set to NA, will print graphics natively |
png_res |
Resolution for png output. |
dynamic_resize |
Factor (>= 0) by which to scale the dynamic resize of the observation heatmap and the overall plot based on how many cells there are. Default is 0, which disables the scaling. Try 1 first if you want to enable. |
ref_contig |
If given, will focus cluster on only genes in this contig. |
write_expr_matrix |
Includes writing a matrix file containing the expression data that is plotted in the heatmap. |
write_phylo |
Write newick strings of the dendrograms displayed on the left side of the heatmap to file. |
useRaster |
Whether to use rasterization for drawing heatmap. Only disable if it produces an error as it is much faster than not using it. |
A list of all relevent settings used for the plotting to be able to reuse them in another plot call while keeping consistant plotting settings, most importantly x.range.
# data(infercnv_data_example) # data(infercnv_annots_example) # data(infercnv_genes_example) # infercnv_object_example <- infercnv::CreateInfercnvObject(raw_counts_matrix=infercnv_data_example, # gene_order_file=infercnv_genes_example, # annotations_file=infercnv_annots_example, # ref_group_names=c("normal")) # infercnv_object_example <- infercnv::run(infercnv_object_example, # cutoff=1, # out_dir=tempfile(), # cluster_by_groups=TRUE, # denoise=TRUE, # HMM=FALSE, # num_threads=2, # no_plot=TRUE) data(infercnv_object_example) plot_cnv(infercnv_object_example, out_dir=tempfile(), obs_title="Observations (Cells)", ref_title="References (Cells)", cluster_by_groups=TRUE, x.center=1, x.range="auto", hclust_method='ward.D', color_safe_pal=FALSE, output_filename="infercnv", output_format="png", png_res=300, dynamic_resize=0 )# data(infercnv_data_example) # data(infercnv_annots_example) # data(infercnv_genes_example) # infercnv_object_example <- infercnv::CreateInfercnvObject(raw_counts_matrix=infercnv_data_example, # gene_order_file=infercnv_genes_example, # annotations_file=infercnv_annots_example, # ref_group_names=c("normal")) # infercnv_object_example <- infercnv::run(infercnv_object_example, # cutoff=1, # out_dir=tempfile(), # cluster_by_groups=TRUE, # denoise=TRUE, # HMM=FALSE, # num_threads=2, # no_plot=TRUE) data(infercnv_object_example) plot_cnv(infercnv_object_example, out_dir=tempfile(), obs_title="Observations (Cells)", ref_title="References (Cells)", cluster_by_groups=TRUE, x.center=1, x.range="auto", hclust_method='ward.D', color_safe_pal=FALSE, output_filename="infercnv", output_format="png", png_res=300, dynamic_resize=0 )
Takes an infercnv object and subdivides it into one object per group of cells to allow plotting of each group on a seperate plot. If references are selected, they will appear on the observation heatmap area as it is larger.
plot_per_group( infercnv_obj, on_references = TRUE, on_observations = TRUE, sample = FALSE, n_cells = 1000, every_n = NULL, above_m = 1000, k_obs_groups = 1, base_filename = "infercnv_per_group", output_format = "png", write_expr_matrix = TRUE, save_objects = FALSE, png_res = 300, dynamic_resize = 0, useRaster = TRUE, out_dir )plot_per_group( infercnv_obj, on_references = TRUE, on_observations = TRUE, sample = FALSE, n_cells = 1000, every_n = NULL, above_m = 1000, k_obs_groups = 1, base_filename = "infercnv_per_group", output_format = "png", write_expr_matrix = TRUE, save_objects = FALSE, png_res = 300, dynamic_resize = 0, useRaster = TRUE, out_dir )
infercnv_obj |
infercnv_object |
on_references |
boolean (default=TRUE), plot references (normal cells). |
on_observations |
boolean (default=TRUE), plot observations data (tumor cells). |
sample |
Whether unique groups of cells should be sampled from or not. (see other parameters for how sampling is done) (Default: FALSE) |
n_cells |
Number of cells that should be sampled per group if sampling is enabled (default = 1000) . |
every_n |
Sample 1 cell every_n cells for each group that has above_m cells, if sampling is enabled. If subclusters are defined, this will make sure that at least one cell per subcluster is sampled. Requires above_m to be set to work, overriding n_cells parameter. (Default: NULL) |
above_m |
Sample only groups that have at least above_m cells if sampling is enabled. (default: 1000) Does not require every_n to be set. |
k_obs_groups |
Number of groups to break each group in with cutree (in the color bars on the left side of the plot only). (Default: 1) |
base_filename |
Base prefix for the output files names. Will be followed by OBS/REF to indidate the type of the group, and the group name. (Default: "infercnv_per_group") |
output_format |
Output format for the figure. Choose between "png", "pdf" and NA. NA means to only write the text outputs without generating the figure itself. (default: "png") |
write_expr_matrix |
Includes writing a matrix file containing the expression data that is plotted in the heatmap. (default: FALSE) |
save_objects |
Whether to save the infercnv objects generated for each group as RDS. (default: FALSE) |
png_res |
Resolution for png output. (Default: 300) |
dynamic_resize |
Factor (>= 0) by which to scale the dynamic resize of the observation heatmap and the overall plot based on how many cells there are. Default is 0, which disables the scaling. Try 1 first if you want to enable. (Default: 0) |
useRaster |
Whether to use rasterization for drawing heatmap. Only disable if it produces an error as it is much faster than not using it. |
out_dir |
Directory in which to save plots and other outputs. |
void
# data(infercnv_data_example) # data(infercnv_annots_example) # data(infercnv_genes_example) # infercnv_object_example <- infercnv::CreateInfercnvObject(raw_counts_matrix=infercnv_data_example, # gene_order_file=infercnv_genes_example, # annotations_file=infercnv_annots_example, # ref_group_names=c("normal")) # infercnv_object_example <- infercnv::run(infercnv_object_example, # cutoff=1, # out_dir=tempfile(), # cluster_by_groups=TRUE, # denoise=TRUE, # HMM=FALSE, # num_threads=2, # no_plot=TRUE) data(infercnv_object_example) infercnv::plot_per_group(infercnv_object_example, out_dir=tempfile())# data(infercnv_data_example) # data(infercnv_annots_example) # data(infercnv_genes_example) # infercnv_object_example <- infercnv::CreateInfercnvObject(raw_counts_matrix=infercnv_data_example, # gene_order_file=infercnv_genes_example, # annotations_file=infercnv_annots_example, # ref_group_names=c("normal")) # infercnv_object_example <- infercnv::run(infercnv_object_example, # cutoff=1, # out_dir=tempfile(), # cluster_by_groups=TRUE, # denoise=TRUE, # HMM=FALSE, # num_threads=2, # no_plot=TRUE) data(infercnv_object_example) infercnv::plot_per_group(infercnv_object_example, out_dir=tempfile())
Formats the data and sends it for plotting.
plot_subclusters( infercnv_obj, out_dir, output_filename = "subcluster_as_annotations" )plot_subclusters( infercnv_obj, out_dir, output_filename = "subcluster_as_annotations" )
infercnv_obj |
infercnv object |
out_dir |
Directory in which to output. |
output_filename |
Filename to save the figure to. |
infercnv_obj the modified infercnv object that was plotted where subclusters are assigned as annotation groups
# data(infercnv_data_example) # data(infercnv_annots_example) # data(infercnv_genes_example) # infercnv_object_example <- infercnv::CreateInfercnvObject(raw_counts_matrix=infercnv_data_example, # gene_order_file=infercnv_genes_example, # annotations_file=infercnv_annots_example, # ref_group_names=c("normal")) # infercnv_object_example <- infercnv::run(infercnv_object_example, # cutoff=1, # out_dir=tempfile(), # cluster_by_groups=TRUE, # denoise=TRUE, # HMM=FALSE, # num_threads=2, # no_plot=TRUE) data(infercnv_object_example) plot_subclusters(infercnv_object_example, out_dir=tempfile(), output_filename="subclusters_as_annotations" )# data(infercnv_data_example) # data(infercnv_annots_example) # data(infercnv_genes_example) # infercnv_object_example <- infercnv::CreateInfercnvObject(raw_counts_matrix=infercnv_data_example, # gene_order_file=infercnv_genes_example, # annotations_file=infercnv_annots_example, # ref_group_names=c("normal")) # infercnv_object_example <- infercnv::run(infercnv_object_example, # cutoff=1, # out_dir=tempfile(), # cluster_by_groups=TRUE, # denoise=TRUE, # HMM=FALSE, # num_threads=2, # no_plot=TRUE) data(infercnv_object_example) plot_subclusters(infercnv_object_example, out_dir=tempfile(), output_filename="subclusters_as_annotations" )
Function doing the actual analysis before calling the plotting functions.
run( infercnv_obj, cutoff = 1, min_cells_per_gene = 3, out_dir = NULL, window_length = 101, smooth_method = c("pyramidinal", "runmeans", "coordinates"), num_ref_groups = NULL, ref_subtract_use_mean_bounds = TRUE, cluster_by_groups = TRUE, cluster_references = TRUE, k_obs_groups = 1, hclust_method = "ward.D2", max_centered_threshold = 3, scale_data = FALSE, HMM = FALSE, HMM_transition_prob = 1e-06, HMM_report_by = c("subcluster", "consensus", "cell"), HMM_type = c("i6", "i3"), HMM_i3_pval = 0.05, HMM_i3_use_KS = FALSE, BayesMaxPNormal = 0.5, sim_method = "meanvar", sim_foreground = FALSE, reassignCNVs = TRUE, analysis_mode = c("subclusters", "samples", "cells"), tumor_subcluster_partition_method = c("leiden", "random_trees", "qnorm", "pheight", "qgamma", "shc"), tumor_subcluster_pval = 0.1, k_nn = 20, leiden_method = c("PCA", "simple"), leiden_function = c("CPM", "modularity"), leiden_resolution = "auto", leiden_method_per_chr = c("simple", "PCA"), leiden_function_per_chr = c("modularity", "CPM"), leiden_resolution_per_chr = 1, per_chr_hmm_subclusters = FALSE, per_chr_hmm_subclusters_references = FALSE, z_score_filter = 0.8, denoise = FALSE, noise_filter = NA, sd_amplifier = 1.5, noise_logistic = FALSE, outlier_method_bound = "average_bound", outlier_lower_bound = NA, outlier_upper_bound = NA, final_scale_limits = NULL, final_center_val = NULL, debug = FALSE, num_threads = 4, plot_steps = FALSE, inspect_subclusters = TRUE, resume_mode = TRUE, png_res = 300, plot_probabilities = TRUE, save_rds = TRUE, save_final_rds = TRUE, diagnostics = FALSE, remove_genes_at_chr_ends = FALSE, prune_outliers = FALSE, mask_nonDE_genes = FALSE, mask_nonDE_pval = 0.05, test.use = "wilcoxon", require_DE_all_normals = "any", hspike_aggregate_normals = FALSE, no_plot = FALSE, no_prelim_plot = FALSE, write_expr_matrix = FALSE, write_phylo = FALSE, output_format = "png", plot_chr_scale = FALSE, chr_lengths = NULL, useRaster = TRUE, up_to_step = 100 )run( infercnv_obj, cutoff = 1, min_cells_per_gene = 3, out_dir = NULL, window_length = 101, smooth_method = c("pyramidinal", "runmeans", "coordinates"), num_ref_groups = NULL, ref_subtract_use_mean_bounds = TRUE, cluster_by_groups = TRUE, cluster_references = TRUE, k_obs_groups = 1, hclust_method = "ward.D2", max_centered_threshold = 3, scale_data = FALSE, HMM = FALSE, HMM_transition_prob = 1e-06, HMM_report_by = c("subcluster", "consensus", "cell"), HMM_type = c("i6", "i3"), HMM_i3_pval = 0.05, HMM_i3_use_KS = FALSE, BayesMaxPNormal = 0.5, sim_method = "meanvar", sim_foreground = FALSE, reassignCNVs = TRUE, analysis_mode = c("subclusters", "samples", "cells"), tumor_subcluster_partition_method = c("leiden", "random_trees", "qnorm", "pheight", "qgamma", "shc"), tumor_subcluster_pval = 0.1, k_nn = 20, leiden_method = c("PCA", "simple"), leiden_function = c("CPM", "modularity"), leiden_resolution = "auto", leiden_method_per_chr = c("simple", "PCA"), leiden_function_per_chr = c("modularity", "CPM"), leiden_resolution_per_chr = 1, per_chr_hmm_subclusters = FALSE, per_chr_hmm_subclusters_references = FALSE, z_score_filter = 0.8, denoise = FALSE, noise_filter = NA, sd_amplifier = 1.5, noise_logistic = FALSE, outlier_method_bound = "average_bound", outlier_lower_bound = NA, outlier_upper_bound = NA, final_scale_limits = NULL, final_center_val = NULL, debug = FALSE, num_threads = 4, plot_steps = FALSE, inspect_subclusters = TRUE, resume_mode = TRUE, png_res = 300, plot_probabilities = TRUE, save_rds = TRUE, save_final_rds = TRUE, diagnostics = FALSE, remove_genes_at_chr_ends = FALSE, prune_outliers = FALSE, mask_nonDE_genes = FALSE, mask_nonDE_pval = 0.05, test.use = "wilcoxon", require_DE_all_normals = "any", hspike_aggregate_normals = FALSE, no_plot = FALSE, no_prelim_plot = FALSE, write_expr_matrix = FALSE, write_phylo = FALSE, output_format = "png", plot_chr_scale = FALSE, chr_lengths = NULL, useRaster = TRUE, up_to_step = 100 )
infercnv_obj |
An infercnv object populated with raw count data |
cutoff |
Cut-off for the min average read counts per gene among reference cells. (default: 1) |
min_cells_per_gene |
minimum number of reference cells requiring expression measurements to include the corresponding gene. default: 3 |
out_dir |
path to directory to deposit outputs (default: NULL, required to provide non NULL) ## Smoothing params |
window_length |
Length of the window for the moving average (smoothing). Should be an odd integer. (default: 101)#' |
smooth_method |
Method to use for smoothing: c(runmeans,pyramidinal,coordinates) default: pyramidinal ##### |
num_ref_groups |
The number of reference groups or a list of indices for each group of reference indices in relation to reference_obs. (default: NULL) |
ref_subtract_use_mean_bounds |
Determine means separately for each ref group, then remove intensities within bounds of means (default: TRUE) Otherwise, uses mean of the means across groups. ############################# |
cluster_by_groups |
If observations are defined according to groups (ie. patients), each group of cells will be clustered separately. (default=FALSE, instead will use k_obs_groups setting) |
cluster_references |
Whether to cluster references within their annotations or not. (dendrogram not displayed) (default: TRUE) |
k_obs_groups |
Number of groups in which to break the observations. (default: 1) |
hclust_method |
Method used for hierarchical clustering of cells. Valid choices are: "ward.D", "ward.D2", "single", "complete", "average", "mcquitty", "median", "centroid". default("ward.D2") |
max_centered_threshold |
The maximum value a value can have after centering. Also sets a lower bound of -1 * this value. (default: 3), can set to a numeric value or "auto" to bound by the mean bounds across cells. Set to NA to turn off. |
scale_data |
perform Z-scaling of logtransformed data (default: FALSE). This may be turned on if you have very different kinds of data for your normal and tumor samples. For example, you need to use GTEx representative normal expression profiles rather than being able to leverage normal single cell data that goes with your experiment. ######################################################################### ## Downstream Analyses (HMM or non-DE-masking) based on tumor subclusters |
HMM |
when set to True, runs HMM to predict CNV level (default: FALSE) |
HMM_transition_prob |
transition probability in HMM (default: 1e-6) |
HMM_report_by |
cell, consensus, subcluster (default: subcluster) Note, reporting is performed entirely separately from the HMM prediction. So, you can predict on subclusters, but get per-cell level reporting (more voluminous output). |
HMM_type |
HMM model type. Options: (i6 or i3): i6: infercnv 6-state model (0, 0.5, 1, 1.5, 2, >2) where state emissions are calibrated based on simulated CNV levels. i3: infercnv 3-state model (del, neutral, amp) configured based on normal cells and HMM_i3_pval |
HMM_i3_pval |
p-value for HMM i3 state overlap (default: 0.05) |
HMM_i3_use_KS |
boolean: use the KS test statistic to estimate mean of amp/del distributions (ala HoneyBadger). (default=TRUE) ## Filtering low-conf HMM preds via BayesNet P(Normal) |
BayesMaxPNormal |
maximum P(Normal) allowed for a CNV prediction according to BayesNet. (default=0.5, note zero turns it off) |
sim_method |
method for calibrating CNV levels in the i6 HMM (default: 'meanvar') |
sim_foreground |
don't use... for debugging, developer option. |
reassignCNVs |
(boolean) Given the CNV associated probability of belonging to each possible state, reassign the state assignments made by the HMM to the state that has the highest probability. (default: TRUE) ###################### ## Tumor subclustering |
analysis_mode |
options(samples|subclusters|cells), Grouping level for image filtering or HMM predictions. default: samples (fastest, but subclusters is ideal) |
tumor_subcluster_partition_method |
method for defining tumor subclusters. Options('leiden', 'random_trees', 'qnorm') leiden: Runs a nearest neighbor search, where communities are then partitionned with the Leiden algorithm. random_trees: Slow, uses permutation statistics w/ tree construction. qnorm: defines tree height based on the quantile defined by the tumor_subcluster_pval |
tumor_subcluster_pval |
max p-value for defining a significant tumor subcluster (default: 0.1) |
k_nn |
number k of nearest neighbors to search for when using the Leiden partition method for subclustering (default: 20) |
leiden_method |
Method used to generate the graph on which the Leiden algorithm is applied, one of "PCA" or "simple". (default: "PCA") |
leiden_function |
Whether to use the Constant Potts Model (CPM) or modularity in igraph. Must be either "CPM" or "modularity". (default: "CPM") |
leiden_resolution |
resolution parameter for the Leiden algorithm using the CPM quality score (default: auto) |
leiden_method_per_chr |
Method used to generate the graph on which the Leiden algorithm is applied for the per chromosome subclustering, one of "PCA" or "simple". (default: "simple") |
leiden_function_per_chr |
Whether to use the Constant Potts Model (CPM) or modularity in igraph for the per chromosome subclustering. Must be either "CPM" or "modularity". (default: "modularity") |
leiden_resolution_per_chr |
resolution parameter for the Leiden algorithm for the per chromosome subclustering (default: 1) |
per_chr_hmm_subclusters |
Run subclustering per chromosome over all cells combined to run the HMM on those subclusters instead. Only applicable when using Leiden subclustering. This should provide enough definition in the predictions while avoiding subclusters that are too small thus providing less evidence to work with. (default: FALSE) |
per_chr_hmm_subclusters_references |
Whether the per chromosome subclustering should also be done on references, which should not have as much variation as observations. (default = FALSE) |
z_score_filter |
Z-score used as a treshold to filter genes used for subclustering. Applied based on reference genes to automatically ignore genes with high expression variability such as MHC genes. (default: 0.8) ############################# ## de-noising parameters #### |
denoise |
If True, turns on denoising according to options below |
noise_filter |
Values +- from the reference cell mean will be set to zero (whitening effect) default(NA, instead will use sd_amplifier below. |
sd_amplifier |
Noise is defined as mean(reference_cells) +- sdev(reference_cells) * sd_amplifier default: 1.5 |
noise_logistic |
use the noise_filter or sd_amplifier based threshold (whichever is invoked) as the midpoint in a logistic model for downscaling values close to the mean. (default: FALSE) ################## ## Outlier pruning |
outlier_method_bound |
Method to use for bounding outlier values. (default: "average_bound") Will preferentially use outlier_lower_bounda and outlier_upper_bound if set. |
outlier_lower_bound |
Outliers below this lower bound will be set to this value. |
outlier_upper_bound |
Outliers above this upper bound will be set to this value. ########################## ## Misc options |
final_scale_limits |
The scale limits for the final heatmap output by the run() method. Default "auto". Alt, c(low,high) |
final_center_val |
Center value for final heatmap output by the run() method. |
debug |
If true, output debug level logging. |
num_threads |
(int) number of threads for parallel steps (default: 4) |
plot_steps |
If true, saves infercnv objects and plots data at the intermediate steps. |
inspect_subclusters |
If true, plot subclusters as annotations after the subclustering step to easily see if the subclustering options are good. (default = TRUE) |
resume_mode |
leverage pre-computed and stored infercnv objects where possible. (default=TRUE) |
png_res |
Resolution for png output. |
plot_probabilities |
option to plot posterior probabilities (default: TRUE) |
save_rds |
Whether to save the current step object results as an .rds file (default: TRUE) |
save_final_rds |
Whether to save the final object results as an .rds file (default: TRUE) |
diagnostics |
option to create diagnostic plots after running the Bayesian model (default: FALSE) ####################### ## Experimental options |
remove_genes_at_chr_ends |
experimental option: If true, removes the window_length/2 genes at both ends of the chromosome. |
prune_outliers |
Define outliers loosely as those that exceed the mean boundaries among all cells. These are set to the bounds. ## experimental opts involving DE analysis |
mask_nonDE_genes |
If true, sets genes not significantly differentially expressed between tumor/normal to the mean value for the complete data set (default: 0.05) |
mask_nonDE_pval |
p-value threshold for defining statistically significant DE genes between tumor/normal |
test.use |
statistical test to use. (default: "wilcoxon") alternatives include 'perm' or 't'.' |
require_DE_all_normals |
If mask_nonDE_genes is set, those genes will be masked only if they are are found as DE according to test.use and mask_nonDE_pval in each of the comparisons to normal cells options: "any", "most", "all" (default: "any") other experimental opts |
hspike_aggregate_normals |
instead of trying to model the different normal groupings individually, just merge them in the hspike. |
no_plot |
don't make any of the images. Instead, generate all non-image outputs as part of the run. (default: FALSE) |
no_prelim_plot |
don't make the preliminary infercnv image (default: FALSE) |
write_expr_matrix |
Whether to write text files with the content of matrices when generating plots (default: FALSE) |
write_phylo |
Whether to write newick strings of the dendrograms displayed on the left side of the heatmap to file (default: FALSE) |
output_format |
Output format for the figure. Choose between "png", "pdf" and NA. NA means to only write the text outputs without generating the figure itself. (default: "png") |
plot_chr_scale |
Whether to scale the chromosme width on the heatmap based on their actual size rather than just the number of expressed genes. |
chr_lengths |
A named list of chromsomes lengths to use when plot_chr_scale=TRUE, or else chromosome size is assumed to be the last chromosome's stop position + 10k bp |
useRaster |
Whether to use rasterization for drawing heatmap. Only disable if it produces an error as it is much faster than not using it. (default: TRUE) |
up_to_step |
run() only up to this exact step number (default: 100 >> 23 steps currently in the process) |
infercnv_obj containing filtered and transformed data
data(infercnv_data_example) data(infercnv_annots_example) data(infercnv_genes_example) infercnv_object_example <- infercnv::CreateInfercnvObject(raw_counts_matrix=infercnv_data_example, gene_order_file=infercnv_genes_example, annotations_file=infercnv_annots_example, ref_group_names=c("normal")) infercnv_object_example <- infercnv::run(infercnv_object_example, cutoff=1, out_dir=tempfile(), cluster_by_groups=TRUE, denoise=TRUE, HMM=FALSE, num_threads=2, analysis_mode="samples", no_plot=TRUE)data(infercnv_data_example) data(infercnv_annots_example) data(infercnv_genes_example) infercnv_object_example <- infercnv::CreateInfercnvObject(raw_counts_matrix=infercnv_data_example, gene_order_file=infercnv_genes_example, annotations_file=infercnv_annots_example, ref_group_names=c("normal")) infercnv_object_example <- infercnv::run(infercnv_object_example, cutoff=1, out_dir=tempfile(), cluster_by_groups=TRUE, denoise=TRUE, HMM=FALSE, num_threads=2, analysis_mode="samples", no_plot=TRUE)
Apply sampling on an infercnv object to reduce the number of cells in it and allow faster plotting or have all groups take up the same height on the heatmap
sample_object( infercnv_obj, n_cells = 100, every_n = NULL, above_m = NULL, on_references = TRUE, on_observations = TRUE )sample_object( infercnv_obj, n_cells = 100, every_n = NULL, above_m = NULL, on_references = TRUE, on_observations = TRUE )
infercnv_obj |
infercnv_object |
n_cells |
Number of cells that should be sampled per group (default = 100). |
every_n |
Sample 1 cell every_n cells for each group. If subclusters are defined, this will make sure that at least one cell per subcluster is sampled. Requires above_m to be set to work, overriding n_cells parameter. |
above_m |
Sample groups that have at least above_m cells. Requires every_n to be set to work, overriding n_cells parameter |
on_references |
boolean (default=TRUE), sample references (normal cells). |
on_observations |
boolean (default=TRUE), sample observations data (tumor cells). |
sampled infercnv_obj
# data(infercnv_data_example) # data(infercnv_annots_example) # data(infercnv_genes_example) # infercnv_object_example <- infercnv::CreateInfercnvObject(raw_counts_matrix=infercnv_data_example, # gene_order_file=infercnv_genes_example, # annotations_file=infercnv_annots_example, # ref_group_names=c("normal")) # infercnv_object_example <- infercnv::run(infercnv_object_example, # cutoff=1, # out_dir=tempfile(), # cluster_by_groups=TRUE, # denoise=TRUE, # HMM=FALSE, # num_threads=2, # no_plot=TRUE) data(infercnv_object_example) infercnv_object_example <- infercnv::sample_object(infercnv_object_example, n_cells=5) # plot result object# data(infercnv_data_example) # data(infercnv_annots_example) # data(infercnv_genes_example) # infercnv_object_example <- infercnv::CreateInfercnvObject(raw_counts_matrix=infercnv_data_example, # gene_order_file=infercnv_genes_example, # annotations_file=infercnv_annots_example, # ref_group_names=c("normal")) # infercnv_object_example <- infercnv::run(infercnv_object_example, # cutoff=1, # out_dir=tempfile(), # cluster_by_groups=TRUE, # denoise=TRUE, # HMM=FALSE, # num_threads=2, # no_plot=TRUE) data(infercnv_object_example) infercnv_object_example <- infercnv::sample_object(infercnv_object_example, n_cells=5) # plot result object
validate an infercnv_obj ensures that order of genes in the @gene_order slot match up perfectly with the gene rows in the @expr.data matrix. Otherwise, throws an error and stops execution.
validate_infercnv_obj(infercnv_obj)validate_infercnv_obj(infercnv_obj)
infercnv_obj |
infercnv_object |
none