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Fix #4: Error when source/target has regex special characters for circos plot #5

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Fix #4: Error when source/target has regex special characters for circos plot #5

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12 changes: 6 additions & 6 deletions R/cc_circos.R
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Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@ cc_circos <- function(cc_df, option = "A", n_top_ints = 15, exp_df = NULL, cell_
stopifnot("'cc_df' must be a dataframe" = is(cc_df, "data.frame"))
stopifnot("cc_df should contain columns named source, target, ligand, receptor and score. See `toy_data` for an example." = all(c('source', 'target', 'ligand', 'receptor', 'score') %in% colnames(cc_df)))
stopifnot("option must be either 'A', 'B', 'C'" = option %in% c('A', 'B', 'C'))

target <- score <- ligand <- receptor <- source_lig <- target_rec <- cell_type <- gene <- cell_gene <- NULL
if (option == "A") {
input_df <- cc_df %>%
Expand All @@ -41,7 +41,7 @@ cc_circos <- function(cc_df, option = "A", n_top_ints = 15, exp_df = NULL, cell_
tally()
if (is.null(cell_cols)) {
cell_cols <- setNames(paletteMartin(n = length(unique(c(input_df$source, input_df$target)))), unique(c(input_df$source, input_df$target)))
}
}
circlize_plot <- function() {
par(cex = cex)
chordDiagram(input_df,
Expand Down Expand Up @@ -99,7 +99,7 @@ cc_circos <- function(cc_df, option = "A", n_top_ints = 15, exp_df = NULL, cell_
)
}, bg.border = NA)
for (l in unique(str_extract(segments, "[^|]+"))) {
highlight.sector(segments[str_detect(segments, paste0("^", l))], track.index = 2, col = cell_cols[l])
highlight.sector(segments[str_detect(segments, paste0("^", str_escape(l)))], track.index = 2, col = cell_cols[l])
}
if (show_legend == TRUE) {
draw(lgd, just = c("left", "bottom"), x = unit(5, "mm"), y = unit(5, "mm"))
Expand All @@ -109,7 +109,7 @@ cc_circos <- function(cc_df, option = "A", n_top_ints = 15, exp_df = NULL, cell_
} else if (option == "C") {
stopifnot("'exp_df' must be a dataframe" = is(exp_df, "data.frame"))
stopifnot("exp_df should contain columns named cell_type, gene and mean_exp. See `toy_exp` for an example." = all(c('cell_type', 'gene', 'mean_exp') %in% colnames(exp_df)))

input_df <- cc_df %>%
slice_max(order_by = score, n = n_top_ints) %>%
mutate(
Expand Down Expand Up @@ -167,7 +167,7 @@ cc_circos <- function(cc_df, option = "A", n_top_ints = 15, exp_df = NULL, cell_
)
}, bg.border = NA)
for (l in unique(str_extract(segments, "[^|]+"))) {
highlight.sector(segments[str_detect(segments, paste0("^", l))], track.index = 2, col = cell_cols[l])
highlight.sector(segments[str_detect(segments, paste0("^", str_escape(l)))], track.index = 2, col = cell_cols[l])
}
circos.track(track.index = 3, panel.fun = function(x, y) {
circos.rect(CELL_META$xlim[1], CELL_META$ylim[1], CELL_META$xlim[2], CELL_META$ylim[2],
Expand All @@ -179,6 +179,6 @@ cc_circos <- function(cc_df, option = "A", n_top_ints = 15, exp_df = NULL, cell_
}
circos.clear()
}
}
}
circlize_plot()
}