| 876 |
876 |
roi ##<< The region of interest.
|
| 877 |
877 |
) {
|
| 878 |
878 |
tr_regions = apply(t(1:length(regions[,1])), 2, function(i) {
|
| 879 |
|
print(i)
|
| 880 |
879 |
tmp_regions_ref2 = list(name="foo", begin=regions[i,]$lower_bound, end=regions[i,]$upper_bound, chr=as.character(regions[i,]$chr), strain_ref = combi[2])
|
| 881 |
880 |
big_roi = roi
|
| 882 |
881 |
trs_tmp_regions_ref2 = translate_roi(tmp_regions_ref2, combi[1], config = config, big_roi = big_roi)
|
| ... | ... | |
| 1833 |
1832 |
plot_ellipse_nucs = TRUE, ##<< Plot (or not) ellipse for a nuc.
|
| 1834 |
1833 |
change_col = TRUE, ##<< Change the color of each nucleosome.
|
| 1835 |
1834 |
plot_wp_nucs = TRUE, ##<< Plot (or not) cluster of nucs
|
|
1835 |
plot_fuzzy_nucs = TRUE, ##<< Plot (or not) cluster of fuzzy
|
| 1836 |
1836 |
plot_wp_nuc_model = TRUE, ##<< Plot (or not) gaussian model for a cluster of nucs
|
| 1837 |
|
plot_common_nucs = TRUE, ##<< Plot (or not) aligned reads.
|
|
1837 |
plot_common_nucs = FALSE, ##<< Plot (or not) aligned reads.
|
|
1838 |
plot_common_unrs = FALSE, ##<< Plot (or not) unaligned nucleosomal refgions (UNRs).
|
| 1838 |
1839 |
plot_wp_nucs_4_nonmnase = FALSE, ##<< Plot (or not) clusters for non inputs samples.
|
| 1839 |
1840 |
plot_chain = FALSE, ##<< Plot (or not) clusterised nuceosomes between mnase samples.
|
| 1840 |
1841 |
aggregated_intra_strain_nucs = NULL, ##<< list of aggregated intra strain nucs. If NULL, it will be computed.
|
| ... | ... | |
| 1865 |
1866 |
axis(2, at=0:(nb_rank_glo*2) * delta_y_glo / (nb_rank_glo*2), labels=c(rep(c(height/2,0),nb_rank_glo),height/2))
|
| 1866 |
1867 |
# Go
|
| 1867 |
1868 |
replicates_wp_nucs = list()
|
|
1869 |
wp_maps = list()
|
|
1870 |
fuzzy_maps = list()
|
| 1868 |
1871 |
for (replicate_rank in 1:length(replicates)) {
|
| 1869 |
1872 |
# Computing replicate parameters
|
| 1870 |
1873 |
nb_rank = length(samples)
|
| ... | ... | |
| 1976 |
1979 |
}
|
| 1977 |
1980 |
|
| 1978 |
1981 |
# Plot wp nucs
|
| 1979 |
|
if ((plot_wp_nucs_4_nonmnase | sample$marker == "Mnase_Seq") & (plot_wp_nucs | plot_common_nucs | plot_chain)) {
|
|
1982 |
if ((plot_wp_nucs_4_nonmnase | sample$marker == "Mnase_Seq") & (plot_wp_nucs | plot_fuzzy_nucs | plot_common_nucs | plot_chain)) {
|
| 1980 |
1983 |
if (samples[[1]]$marker == "Mnase_Seq") {
|
| 1981 |
1984 |
if (is.null(aggregated_intra_strain_nucs)) {
|
| 1982 |
1985 |
wp_nucs = aggregate_intra_strain_nucs(samples)[[1]]
|
| ... | ... | |
| 2028 |
2031 |
text(tmp_x_inter, tmp_y_inter, tmp_lod_inter, srt=90, cex=0.9, bg = "yellow")#, col=(tmp_lod_inter < 20) + 2)
|
| 2029 |
2032 |
}
|
| 2030 |
2033 |
|
| 2031 |
|
if (plot_wp_nucs | plot_common_nucs ) {
|
|
2034 |
if (plot_wp_nucs | plot_fuzzy_nucs | plot_common_nucs ) {
|
| 2032 |
2035 |
replicates_wp_nucs[[replicate_rank]] = wp_nucs
|
| 2033 |
|
for (wp_nuc in wp_nucs) {
|
| 2034 |
|
if (wp_nuc$wp){
|
| 2035 |
|
rect(sign(x_min) * wp_nuc$lower_bound + shift, y_min, sign(x_min) * wp_nuc$upper_bound + shift, y_max, col=adjustcolor(2, alpha.f = 0.1), border=1)
|
| 2036 |
|
all_original_reads = c()
|
| 2037 |
|
for(initial_nuc in wp_nuc$nucs) {
|
| 2038 |
|
all_original_reads = c(all_original_reads, initial_nuc$original_reads)
|
| 2039 |
|
}
|
| 2040 |
|
delta_x = wp_nuc$lower_bound:wp_nuc$upper_bound
|
| 2041 |
|
if (FALSE) {
|
| 2042 |
|
rect(sign(x_min) * wp_nuc$lower_bound + shift, y_min, sign(x_min) * wp_nuc$upper_bound + shift, y_max, col="#EEEEEE", border=1)
|
| 2043 |
|
}
|
| 2044 |
|
if (plot_wp_nuc_model) {
|
| 2045 |
|
lines(sign(x_min) * delta_x + shift, dnorm(delta_x, mean(all_original_reads), sd(all_original_reads)) * length(all_original_reads) * height/5 + y_min, col=1)
|
|
2036 |
strain = samples[[1]]$strain
|
|
2037 |
wp_maps[[strain]] = flat_aggregated_intra_strain_nucs(wp_nucs, "foo")
|
|
2038 |
fuzzy_maps[[strain]] = get_intra_strain_fuzzy(wp_maps[[strain]], as.list(samples[[1]]$roi), samples[[1]]$strain, config=config)
|
|
2039 |
|
|
2040 |
if (plot_fuzzy_nucs) {
|
|
2041 |
fuzzy_map = fuzzy_maps[[strain]]
|
|
2042 |
rect(sign(x_min) * fuzzy_map$lower_bound + shift, y_min, sign(x_min) * fuzzy_map$upper_bound + shift, y_max, col=adjustcolor(3, alpha.f = 0.1), border=1)
|
|
2043 |
}
|
|
2044 |
|
|
2045 |
if (plot_wp_nucs) {
|
|
2046 |
for (wp_nuc in wp_nucs) {
|
|
2047 |
if (wp_nuc$wp){
|
|
2048 |
rect(sign(x_min) * wp_nuc$lower_bound + shift, y_min, sign(x_min) * wp_nuc$upper_bound + shift, y_max, col=adjustcolor(2, alpha.f = 0.1), border=1)
|
|
2049 |
if (plot_wp_nuc_model) {
|
|
2050 |
all_original_reads = c()
|
|
2051 |
for(initial_nuc in wp_nuc$nucs) {
|
|
2052 |
all_original_reads = c(all_original_reads, initial_nuc$original_reads)
|
|
2053 |
}
|
|
2054 |
delta_x = wp_nuc$lower_bound:wp_nuc$upper_bound
|
|
2055 |
lines(sign(x_min) * delta_x + shift, dnorm(delta_x, mean(all_original_reads), sd(all_original_reads)) * length(all_original_reads) * height/5 + y_min, col=1)
|
|
2056 |
}
|
| 2046 |
2057 |
}
|
| 2047 |
2058 |
}
|
| 2048 |
2059 |
}
|
| ... | ... | |
| 2051 |
2062 |
}
|
| 2052 |
2063 |
|
| 2053 |
2064 |
if (plot_common_nucs) {
|
| 2054 |
|
if (is.null(aligned_inter_strain_nucs)) {
|
| 2055 |
|
aligned_inter_strain_nucs = align_inter_strain_nucs(replicates, replicates_wp_nucs[[1]], replicates_wp_nucs[[2]], config=config)[[1]]
|
| 2056 |
|
}
|
| 2057 |
|
if (plot_common_nucs) {
|
| 2058 |
|
#Plot common wp nucs
|
| 2059 |
|
mid_y = shift = x_min = x_max = nb_rank = base = ylim = ymin = y_max = delta_y = list()
|
| 2060 |
|
for (replicate_rank in 1:length(replicates)) {
|
| 2061 |
|
nb_rank[[replicate_rank]] = length(samples)
|
| 2062 |
|
base[[replicate_rank]] = (replicate_rank-1) * height * nb_rank[[replicate_rank]]
|
| 2063 |
|
ylim[[replicate_rank]] = c(base[[replicate_rank]], base[[replicate_rank]] + height * nb_rank[[replicate_rank]])
|
| 2064 |
|
y_min[[replicate_rank]] = min(ylim[[replicate_rank]])
|
| 2065 |
|
y_max[[replicate_rank]] = max(ylim[[replicate_rank]])
|
| 2066 |
|
delta_y[[replicate_rank]] = y_max[[replicate_rank]] - y_min[[replicate_rank]]
|
| 2067 |
|
mid_y[[replicate_rank]] = (y_max[[replicate_rank]] + y_min[[replicate_rank]]) / 2
|
|
2065 |
if (is.null(aligned_inter_strain_nucs)) {
|
|
2066 |
aligned_inter_strain_nucs = align_inter_strain_nucs(replicates, replicates_wp_nucs[[1]], replicates_wp_nucs[[2]], config=config)[[1]]
|
|
2067 |
aligned_inter_strain_nucs$roi_index = "foo"
|
|
2068 |
}
|
| 2068 |
2069 |
|
| 2069 |
|
samples = replicates[[replicate_rank]]
|
| 2070 |
|
for (sample_rank in 1:length(samples)) {
|
| 2071 |
|
sample = samples[[sample_rank]]
|
| 2072 |
|
y_lev = y_min[[replicate_rank]] + (sample_rank - 0.5) * delta_y[[replicate_rank]]/nb_rank[[replicate_rank]]
|
| 2073 |
|
if (sample$roi[["begin"]] < sample$roi[["end"]]) {
|
| 2074 |
|
x_min[[replicate_rank]] = sample$roi[["begin"]]
|
| 2075 |
|
x_max[[replicate_rank]] = sample$roi[["end"]]
|
| 2076 |
|
} else {
|
| 2077 |
|
x_min[[replicate_rank]] = - sample$roi[["begin"]]
|
| 2078 |
|
x_max[[replicate_rank]] = - sample$roi[["end"]]
|
| 2079 |
|
}
|
| 2080 |
|
shift[[replicate_rank]] = x_min[[1]] - x_min[[replicate_rank]]
|
|
2070 |
#Plot common wp nucs
|
|
2071 |
mid_y = shift = x_min = x_max = nb_rank = base = ylim = ymin = y_max = delta_y = list()
|
|
2072 |
for (replicate_rank in 1:length(replicates)) {
|
|
2073 |
nb_rank[[replicate_rank]] = length(samples)
|
|
2074 |
base[[replicate_rank]] = (replicate_rank-1) * height * nb_rank[[replicate_rank]]
|
|
2075 |
ylim[[replicate_rank]] = c(base[[replicate_rank]], base[[replicate_rank]] + height * nb_rank[[replicate_rank]])
|
|
2076 |
y_min[[replicate_rank]] = min(ylim[[replicate_rank]])
|
|
2077 |
y_max[[replicate_rank]] = max(ylim[[replicate_rank]])
|
|
2078 |
delta_y[[replicate_rank]] = y_max[[replicate_rank]] - y_min[[replicate_rank]]
|
|
2079 |
mid_y[[replicate_rank]] = (y_max[[replicate_rank]] + y_min[[replicate_rank]]) / 2
|
|
2080 |
|
|
2081 |
samples = replicates[[replicate_rank]]
|
|
2082 |
for (sample_rank in 1:length(samples)) {
|
|
2083 |
sample = samples[[sample_rank]]
|
|
2084 |
y_lev = y_min[[replicate_rank]] + (sample_rank - 0.5) * delta_y[[replicate_rank]]/nb_rank[[replicate_rank]]
|
|
2085 |
if (sample$roi[["begin"]] < sample$roi[["end"]]) {
|
|
2086 |
x_min[[replicate_rank]] = sample$roi[["begin"]]
|
|
2087 |
x_max[[replicate_rank]] = sample$roi[["end"]]
|
|
2088 |
} else {
|
|
2089 |
x_min[[replicate_rank]] = - sample$roi[["begin"]]
|
|
2090 |
x_max[[replicate_rank]] = - sample$roi[["end"]]
|
| 2081 |
2091 |
}
|
|
2092 |
shift[[replicate_rank]] = x_min[[1]] - x_min[[replicate_rank]]
|
| 2082 |
2093 |
}
|
| 2083 |
|
for (inter_strain_nuc_index in 1:length(aligned_inter_strain_nucs[,1])) {
|
| 2084 |
|
inter_strain_nuc = aligned_inter_strain_nucs[inter_strain_nuc_index,]
|
| 2085 |
|
tmp_xs = tmp_ys = c()
|
| 2086 |
|
for (replicate_rank in 1:length(replicates)) {
|
| 2087 |
|
samples = replicates[[replicate_rank]]
|
| 2088 |
|
strain = samples[[1]]$strain
|
| 2089 |
|
tmp_xs = c(tmp_xs, sign(x_min[[replicate_rank]]) * (inter_strain_nuc[[paste("lower_bound_",strain,sep="")]] + inter_strain_nuc[[paste("upper_bound_",strain,sep="")]])/2 + shift[[replicate_rank]])
|
| 2090 |
|
tmp_ys = c(tmp_ys, mid_y[[replicate_rank]])
|
| 2091 |
|
}
|
| 2092 |
|
lines(tmp_xs, tmp_ys, col=2, type="b", lwd=dev.size()[1]*100/(x_max[[1]]-x_min[[1]]), cex=dev.size()[1]*200/(x_max[[1]]-x_min[[1]]), pch=19)
|
|
2094 |
}
|
|
2095 |
for (inter_strain_nuc_index in 1:length(aligned_inter_strain_nucs[,1])) {
|
|
2096 |
inter_strain_nuc = aligned_inter_strain_nucs[inter_strain_nuc_index,]
|
|
2097 |
tmp_xs = tmp_ys = c()
|
|
2098 |
for (replicate_rank in 1:length(replicates)) {
|
|
2099 |
samples = replicates[[replicate_rank]]
|
|
2100 |
strain = samples[[1]]$strain
|
|
2101 |
tmp_xs = c(tmp_xs, sign(x_min[[replicate_rank]]) * (inter_strain_nuc[[paste("lower_bound_",strain,sep="")]] + inter_strain_nuc[[paste("upper_bound_",strain,sep="")]])/2 + shift[[replicate_rank]])
|
|
2102 |
tmp_ys = c(tmp_ys, mid_y[[replicate_rank]])
|
| 2093 |
2103 |
}
|
| 2094 |
|
}
|
|
2104 |
lines(tmp_xs, tmp_ys, col=2, type="b", lwd=dev.size()[1]*100/(x_max[[1]]-x_min[[1]]), cex=dev.size()[1]*200/(x_max[[1]]-x_min[[1]]), pch=19)
|
|
2105 |
}
|
|
2106 |
|
|
2107 |
if (plot_common_unrs) {
|
|
2108 |
combi = c(replicates[[1]][[1]]$strain, replicates[[2]][[1]]$strain)
|
|
2109 |
roi = as.list(samples[[1]]$roi)
|
|
2110 |
roi_index = "foo"
|
|
2111 |
common_nuc_results = list()
|
|
2112 |
common_nuc_results[[paste(combi[1], combi[2], sep="_")]] = aligned_inter_strain_nucs
|
|
2113 |
unrs = get_unrs(combi, roi, roi_index, wp_maps, fuzzy_maps, common_nuc_results, config = config)
|
|
2114 |
rect(sign(x_min[[1]]) * unrs$lower_bound + shift[[1]], y_min[[1]], sign(x_min[[1]]) * unrs$upper_bound + shift[[1]], y_max[[2]], col=adjustcolor(4, alpha.f = 0.3), border=1)
|
|
2115 |
}
|
|
2116 |
|
| 2095 |
2117 |
}
|
| 2096 |
2118 |
return(returned_list)
|
| 2097 |
2119 |
}
|
| 2098 |
2120 |
|
| 2099 |
2121 |
|
| 2100 |
2122 |
|
|
2123 |
get_intra_strain_fuzzy = function(# Compute the fuzzy list for a given strain.
|
|
2124 |
### This function grabs the nucleosomes detxted by template_filter that have been rejected bt aggregate_intra_strain_nucs as well positions.
|
|
2125 |
wp_maps, ##<< Well positionned nucleosomes map.
|
|
2126 |
roi, ##<< The region of interest.
|
|
2127 |
strain, ##<< The strain we want to extracvt the fuzzy map.
|
|
2128 |
config=NULL ##<< GLOBAL config variable.
|
|
2129 |
) {
|
|
2130 |
fuzzy_map = wp_map[wp_map$wp==0, ]
|
|
2131 |
if (nrow(fuzzy_map) > 0) {
|
|
2132 |
fuzzy_map = substract_region(fuzzy_map, wp_map[wp_map$wp==1,])
|
|
2133 |
if (!is.null(fuzzy_map)) {
|
|
2134 |
fuzzy_map = union_regions(fuzzy_map)
|
|
2135 |
fuzzy_map = crop_fuzzy(fuzzy_map, roi, strain, config)
|
|
2136 |
}
|
|
2137 |
}
|
|
2138 |
return(fuzzy_map)
|
|
2139 |
}
|
|
2140 |
|
|
2141 |
|
|
2142 |
|
|
2143 |
|
|
2144 |
|
|
2145 |
get_unrs = function(# Compute the unaligned nucleosomal regions (UNRs).
|
|
2146 |
### This function aggregate non common wp nucs for each strain and substract common wp nucs. It does not take care about the size of the resulting UNR. It will be take into account in the count read part og the pipeline.
|
|
2147 |
combi, ##<< The strain combination to consider.
|
|
2148 |
roi, ##<< The region of interest.
|
|
2149 |
roi_index, ##<< The region of interest index.
|
|
2150 |
wp_maps, ##<< Well positionned nucleosomes maps.
|
|
2151 |
fuzzy_maps, ##<< Fuzzy nucleosomes maps.
|
|
2152 |
common_nuc_results, ##<< Common wp nuc maps
|
|
2153 |
config=NULL ##<< GLOBAL config variable
|
|
2154 |
) {
|
|
2155 |
print(roi_index)
|
|
2156 |
|
|
2157 |
tmp_combi_key = paste(combi[1], combi[2], sep="_")
|
|
2158 |
tmp_common_nucs = common_nuc_results[[tmp_combi_key]]
|
|
2159 |
tmp_common_nucs = tmp_common_nucs[tmp_common_nucs$roi_index == roi_index, ]
|
|
2160 |
|
|
2161 |
print(paste("Dealing with unr from", combi[1]))
|
|
2162 |
tmp_fuzzy = fuzzy_maps[[combi[1]]]
|
|
2163 |
tmp_fuzzy = tmp_fuzzy[tmp_fuzzy$roi_index == roi_index, ]
|
|
2164 |
tmp_wp = wp_maps[[combi[1]]]
|
|
2165 |
tmp_wp = tmp_wp[tmp_wp$wp==1,]
|
|
2166 |
tmp_wp = tmp_wp[tmp_wp$roi_index == roi_index, ]
|
|
2167 |
# Let's go!
|
|
2168 |
tmp_index = unlist(apply(t(tmp_wp$index_nuc), 2, function(index_nuc) {
|
|
2169 |
if (index_nuc %in% tmp_common_nucs[[paste("index_nuc", combi[1], sep="_")]]) {
|
|
2170 |
return(NULL)
|
|
2171 |
} else {
|
|
2172 |
return (index_nuc)
|
|
2173 |
}
|
|
2174 |
}))
|
|
2175 |
tmp_unaligned_wp = tmp_wp[tmp_wp$index_nuc %in% tmp_index, ]
|
|
2176 |
tmp_unr = rbind(tmp_fuzzy,tmp_unaligned_wp[,1:4])
|
|
2177 |
if (length(tmp_unr) != 0) {
|
|
2178 |
tmp_unr = union_regions(tmp_unr)
|
|
2179 |
}
|
|
2180 |
tmp_unr_nucs_1 = tmp_unr
|
|
2181 |
if (length(tmp_unr_nucs_1[,1]) == 0) {return(NULL)}
|
|
2182 |
agg_unr_1 = tmp_unr_nucs_1
|
|
2183 |
|
|
2184 |
print(paste("Dealing with unr from ", combi[2]))
|
|
2185 |
tmp_fuzzy = fuzzy_maps[[combi[2]]]
|
|
2186 |
tmp_fuzzy = tmp_fuzzy[tmp_fuzzy$roi_index == roi_index, ]
|
|
2187 |
tmp_wp = wp_maps[[combi[2]]]
|
|
2188 |
tmp_wp = tmp_wp[tmp_wp$wp==1,]
|
|
2189 |
tmp_wp = tmp_wp[tmp_wp$roi_index == roi_index, ]
|
|
2190 |
# Let's go!
|
|
2191 |
tmp_index = unlist(apply(t(tmp_wp$index_nuc), 2, function(index_nuc) {
|
|
2192 |
if (index_nuc %in% tmp_common_nucs[[paste("index_nuc", combi[2], sep="_")]]) {
|
|
2193 |
return(NULL)
|
|
2194 |
} else {
|
|
2195 |
return (index_nuc)
|
|
2196 |
}
|
|
2197 |
}))
|
|
2198 |
tmp_unaligned_wp = tmp_wp[tmp_wp$index_nuc %in% tmp_index, ]
|
|
2199 |
tmp_unr = rbind(tmp_fuzzy,tmp_unaligned_wp[,1:4])
|
|
2200 |
if (length(tmp_unr) != 0) {
|
|
2201 |
tmp_unr = union_regions(tmp_unr)
|
|
2202 |
}
|
|
2203 |
tmp_unr_nucs_2 = tmp_unr
|
|
2204 |
if (length(tmp_unr_nucs_2[,1]) == 0) {return(NULL)}
|
|
2205 |
agg_unr_2 = crop_fuzzy(tmp_unr_nucs_2, roi, combi[2], config)
|
|
2206 |
tr_agg_unr_2 = translate_regions(agg_unr_2, combi, roi_index, roi=roi, config=config)
|
|
2207 |
tr_agg_unr_2 = union_regions(tr_agg_unr_2)
|
|
2208 |
|
|
2209 |
print("Dealing with unr from both...")
|
|
2210 |
all_unr = union_regions(rbind(agg_unr_1, tr_agg_unr_2))
|
|
2211 |
|
|
2212 |
print(paste("Dealing with wp from", combi[1]))
|
|
2213 |
tmp_wp = wp_maps[[combi[1]]]
|
|
2214 |
tmp_wp = tmp_wp[tmp_wp$wp==1,]
|
|
2215 |
tmp_wp = tmp_wp[tmp_wp$roi_index == roi_index, ]
|
|
2216 |
# Let's go!
|
|
2217 |
tmp_index = unlist(apply(t(tmp_wp$index_nuc), 2, function(index_nuc) {
|
|
2218 |
if (index_nuc %in% tmp_common_nucs[[paste("index_nuc", combi[1], sep="_")]]) {
|
|
2219 |
return (index_nuc)
|
|
2220 |
} else {
|
|
2221 |
return(NULL)
|
|
2222 |
}
|
|
2223 |
}))
|
|
2224 |
wp_nucs_1 = tmp_wp[tmp_wp$index_nuc %in% tmp_index, ]
|
|
2225 |
|
|
2226 |
print(paste("Dealing with wp from", combi[2]))
|
|
2227 |
tmp_wp = wp_maps[[combi[2]]]
|
|
2228 |
tmp_wp = tmp_wp[tmp_wp$wp==1,]
|
|
2229 |
tmp_wp = tmp_wp[tmp_wp$roi_index == roi_index, ]
|
|
2230 |
# Let's go!
|
|
2231 |
tmp_index = unlist(apply(t(tmp_wp$index_nuc), 2, function(index_nuc) {
|
|
2232 |
if (index_nuc %in% tmp_common_nucs[[paste("index_nuc", combi[2], sep="_")]]) {
|
|
2233 |
return (index_nuc)
|
|
2234 |
} else {
|
|
2235 |
return(NULL)
|
|
2236 |
}
|
|
2237 |
}))
|
|
2238 |
wp_nucs_2 = tmp_wp[tmp_wp$index_nuc %in% tmp_index, ]
|
|
2239 |
wp_nucs_2 = crop_fuzzy(wp_nucs_2, roi, combi[2], config)
|
|
2240 |
if (nrow(wp_nucs_2) == 0) {
|
|
2241 |
tr_wp_nucs_2 = wp_nucs_2
|
|
2242 |
} else {
|
|
2243 |
tr_wp_nucs_2 = translate_regions(wp_nucs_2, combi, roi_index, roi=roi, config=config)
|
|
2244 |
}
|
|
2245 |
|
|
2246 |
print("Dealing with wp from both...")
|
|
2247 |
all_wp = union_regions(rbind(wp_nucs_1[,1:4], tr_wp_nucs_2))
|
|
2248 |
|
|
2249 |
print("Dealing with unr and wp...")
|
|
2250 |
non_inter_unr = substract_region(all_unr, all_wp)
|
|
2251 |
non_inter_unr = crop_fuzzy(non_inter_unr, roi, combi[1], config)
|
|
2252 |
if (is.null(non_inter_unr)) { return(NULL) }
|
|
2253 |
non_inter_unr$len = non_inter_unr$upper_bound - non_inter_unr$lower_bound
|
|
2254 |
# non_inter_fuzzy = non_inter_fuzzy[non_inter_fuzzy$len >= min_fuzz_width,]
|
|
2255 |
|
|
2256 |
non_inter_unr$index_nuc = 1:length(non_inter_unr[,1])
|
|
2257 |
return (non_inter_unr)
|
|
2258 |
}
|
|
2259 |
|
|
2260 |
|
| 2101 |
2261 |
|