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Connection table fix #8

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merged 5 commits into from
Jan 13, 2020
+22 −12
Merged

Connection table fix #8

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31216d3
- Use ConnectsTo to return info about connectivity in all the ROIs
romainFr Jan 8, 2020
923c990
Can now input a ROI (or a vector of ROIs). Still need to double check…
romainFr Jan 8, 2020
be0d41c
Fix type for the weight column
romainFr Jan 8, 2020
3e56279
Small doc edit
romainFr Jan 8, 2020
17006ac
Merge branch 'master' into connectionTableFix
romainFr Jan 13, 2020
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34 changes: 22 additions & 12 deletions R/connectivity.R
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Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,7 @@ neuprint_get_adjacency_matrix <- function(bodyids, dataset = NULL, all_segments
#' @inheritParams neuprint_find_neurons
#' @param prepost whether to look for partners presynaptic to postsynaptic to the given bodyids
#' @param progress default FALSE. If TRUE, the API is called separately for each neuron and yuo can asses its progress, if an error is thrown by any one bodyid, that bodyid is ignored
#' @return a data frame giving partners within an ROI, the connection strength for weights to or from that partner, and the direction, for the given bodyid
#' @return a data frame giving partners within a set of ROIs, the connection strength for weights to or from that partner, and the direction, for the given bodyid
#' @seealso \code{\link{neuprint_fetch_custom}}, \code{\link{neuprint_simple_connectivity}}, \code{\link{neuprint_common_connectivity}}
#' @export
#' @rdname neuprint_connection_table
Expand Down Expand Up @@ -70,21 +70,31 @@ neuprint_connection_table <- function(bodyids, prepost = c("PRE","POST"), roi =
return(d)
}
dp=neuprint_dataset_prefix(dataset, conn=conn)
prefixed=paste0(dp, "_",all_segments.json)
cypher = sprintf("WITH %s AS bodyIds UNWIND bodyIds AS bodyId MATCH (a:`%s`)<-[:From]-(c:ConnectionSet)-[:To]->(b:`%s`), (c)-[:Contains]->(s:Synapse) WHERE %s (s.type='post') AND %s.bodyId=bodyId RETURN a.bodyId AS %s, b.bodyId AS %s, count(*) AS weight",

prefixed=paste0(dp, all_segments.json)
cypher = sprintf(paste("WITH %s AS bodyIds UNWIND bodyIds AS bodyId",
"MATCH (a:`%s`)-[c:ConnectsTo]->(b:`%s`)",
"WHERE %s.bodyId=bodyId",
"UNWIND %s AS k",
"RETURN a.bodyId AS %s, b.bodyId AS %s, k AS roi,",
"apoc.convert.fromJsonMap(c.roiInfo)[k].post AS weight"),
jsonlite::toJSON(unique(as.numeric(unlist(bodyids)))),
prefixed,
prefixed,
ifelse(is.null(roi),"",sprintf("(exists(s.`%s`)) AND",roi)),
ifelse(prepost=="POST","b","a"),
ifelse(prepost=="POST","partner","bodyid"),
ifelse(prepost=="POST","bodyid","partner"))
ifelse(prepost=="POST","a","b"),
ifelse(is.null(roi),"keys(apoc.convert.fromJsonMap(c.roiInfo))",paste("['",paste(roi,collapse="','"),"']",sep="")),
ifelse(prepost=="POST","bodyid","partner"),
ifelse(prepost=="POST","partner","bodyid")
)
nc = neuprint_fetch_custom(cypher=cypher, conn = conn)
d = data.frame(do.call(rbind,lapply(nc$data,unlist)))
colnames(d) = unlist(nc$columns)
d$prepost = ifelse(prepost=="PRE",0,1)
d = d[order(d$weight,decreasing=TRUE),]
d[,c("bodyid", "partner", "weight", "prepost")]
## Filter out the rare cases where PSDs and tbars are in different ROIs (hence post is null)
nc$data <- nc$data[sapply(nc$data,function(x) !is.null(x[[4]]))]
d <- data.frame(do.call(rbind,lapply(nc$data,unlist)),stringsAsFactors = FALSE)
colnames(d) <- unlist(nc$columns)
d$weight <- as.integer(d$weight)
d$prepost <- ifelse(prepost=="PRE",0,1)
d <- d[order(d$weight,decreasing=TRUE),]
d[,c("bodyid", "partner", "roi","weight", "prepost")]
}

#' @title Get the common synaptic partners for a set of neurons
Expand Down