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Auto updated the code style with https://github.com/LieberInstitute/D…
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…LPFC_snRNAseq/blob/main/code/update_style.R
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@lcolladotor
lcolladotor committed Feb 16, 2023
1 parent d45245e commit 3d66809
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98 changes: 51 additions & 47 deletions code/03_build_sce/08_cluster_annotation.R
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Original file line number Diff line number Diff line change
Expand Up @@ -303,16 +303,16 @@ my_plotMarkers(

#### Assign annotation ####
order_cell_types <- function(cell_types) {
cell_types <- unique(cell_types)
neun_mask <- grepl("Excit|Inhib", cell_types)
drop_mask <- grepl("Ambiguous|drop", cell_types)
neun_ct <- cell_types[neun_mask]
glia_ct <- cell_types[!(neun_mask|drop_mask)]
drop_ct <- cell_types[drop_mask]
ordered_cell_types <- c(sort(glia_ct), sort(neun_ct), sort(drop_ct))
return(ordered_cell_types)
cell_types <- unique(cell_types)
neun_mask <- grepl("Excit|Inhib", cell_types)
drop_mask <- grepl("Ambiguous|drop", cell_types)

neun_ct <- cell_types[neun_mask]
glia_ct <- cell_types[!(neun_mask | drop_mask)]
drop_ct <- cell_types[drop_mask]

ordered_cell_types <- c(sort(glia_ct), sort(neun_ct), sort(drop_ct))
return(ordered_cell_types)
}

## mbkm annotation
Expand All @@ -328,23 +328,25 @@ anno_k2 <- anno_k %>%
ct = paste0(broad, "_", f_pad_zero(row_number(), width = 2)),
n = n()
) %>%
ungroup() %>%
mutate(cellType = ifelse(n > 1, ct, broad),
cellType = factor(cellType, levels = order_cell_types(cellType)),
broad = factor(broad, levels = order_cell_types(broad)))
ungroup() %>%
mutate(
cellType = ifelse(n > 1, ct, broad),
cellType = factor(cellType, levels = order_cell_types(cellType)),
broad = factor(broad, levels = order_cell_types(broad))
)

levels(anno_k2$broad)
# [1] "Astro" "EndoMural" "MicroOligo" "Oligo" "OPC" "Excit" "Inhib" "drop"
# [1] "Astro" "EndoMural" "MicroOligo" "Oligo" "OPC" "Excit" "Inhib" "drop"
levels(anno_k2$cellType)
# [1] "Astro" "EndoMural" "MicroOligo" "Oligo_01" "Oligo_02" "OPC" "Excit_01" "Excit_02"
# [9] "Excit_03" "Excit_04" "Excit_05" "Excit_06" "Excit_07" "Excit_08" "Excit_09" "Excit_10"
# [17] "Excit_11" "Excit_12" "Excit_13" "Inhib_01" "Inhib_02" "Inhib_03" "Inhib_04" "Inhib_05"
# [25] "Inhib_06" "drop_01" "drop_02" "drop_03" "drop_04"
# [1] "Astro" "EndoMural" "MicroOligo" "Oligo_01" "Oligo_02" "OPC" "Excit_01" "Excit_02"
# [9] "Excit_03" "Excit_04" "Excit_05" "Excit_06" "Excit_07" "Excit_08" "Excit_09" "Excit_10"
# [17] "Excit_11" "Excit_12" "Excit_13" "Inhib_01" "Inhib_02" "Inhib_03" "Inhib_04" "Inhib_05"
# [25] "Inhib_06" "drop_01" "drop_02" "drop_03" "drop_04"

## HC annotation
anno_hc <- read.csv(here("processed-data", "03_build_sce", "DLPFC_HC_anno.csv"))
table(anno_hc$broad)
# Ambiguous Astro EndoMural Excit Inhib Micro Oligo OPC
# Ambiguous Astro EndoMural Excit Inhib Micro Oligo OPC
# 1 1 2 15 6 1 3 1

anno_hc2 <- anno_hc %>%
Expand All @@ -354,61 +356,63 @@ anno_hc2 <- anno_hc %>%
n = n()
) %>%
ungroup() %>%
mutate(cellType = ifelse(n > 1, ct, broad),
cellType = factor(cellType, levels = order_cell_types(cellType)),
broad = factor(broad, levels = order_cell_types(broad)))
mutate(
cellType = ifelse(n > 1, ct, broad),
cellType = factor(cellType, levels = order_cell_types(cellType)),
broad = factor(broad, levels = order_cell_types(broad))
)

levels(anno_hc2$broad)
# [1] "Astro" "EndoMural" "Micro" "Oligo" "OPC" "Excit" "Inhib" "Ambiguous"
levels(anno_hc2$cellType)
# [1] "Astro" "EndoMural_01" "EndoMural_02" "Micro" "Oligo_01" "Oligo_02" "Oligo_03"
# [8] "OPC" "Excit_01" "Excit_02" "Excit_03" "Excit_04" "Excit_05" "Excit_06"
# [15] "Excit_07" "Excit_08" "Excit_09" "Excit_10" "Excit_11" "Excit_12" "Excit_13"
# [22] "Excit_14" "Excit_15" "Inhib_01" "Inhib_02" "Inhib_03" "Inhib_04" "Inhib_05"
# [1] "Astro" "EndoMural_01" "EndoMural_02" "Micro" "Oligo_01" "Oligo_02" "Oligo_03"
# [8] "OPC" "Excit_01" "Excit_02" "Excit_03" "Excit_04" "Excit_05" "Excit_06"
# [15] "Excit_07" "Excit_08" "Excit_09" "Excit_10" "Excit_11" "Excit_12" "Excit_13"
# [22] "Excit_14" "Excit_15" "Inhib_01" "Inhib_02" "Inhib_03" "Inhib_04" "Inhib_05"
# [29] "Inhib_06" "Ambiguous"

## Assign to sce
sce$cellType_broad_k <- anno_k2$broad[match(sce$kmeans, anno_k$cluster)]
sce$cellType_k <- anno_k2$cellType[match(sce$kmeans, anno_k2$cluster)]

table(sce$cellType_broad_k)
# Astro EndoMural MicroOligo Oligo OPC Excit Inhib drop
# Astro EndoMural MicroOligo Oligo OPC Excit Inhib drop
# 3557 1330 5541 33716 1791 21233 10413 23

table(sce$cellType_k)
# Astro EndoMural MicroOligo Oligo_01 Oligo_02 OPC Excit_01 Excit_02 Excit_03 Excit_04
# 3557 1330 5541 28085 5631 1791 5879 1058 548 1188
# Excit_05 Excit_06 Excit_07 Excit_08 Excit_09 Excit_10 Excit_11 Excit_12 Excit_13 Inhib_01
# 82 633 3198 2851 896 1581 1732 1292 295 132
# Inhib_02 Inhib_03 Inhib_04 Inhib_05 Inhib_06 drop_01 drop_02 drop_03 drop_04
# 461 2242 6018 1311 249 11 3 2 7
# Astro EndoMural MicroOligo Oligo_01 Oligo_02 OPC Excit_01 Excit_02 Excit_03 Excit_04
# 3557 1330 5541 28085 5631 1791 5879 1058 548 1188
# Excit_05 Excit_06 Excit_07 Excit_08 Excit_09 Excit_10 Excit_11 Excit_12 Excit_13 Inhib_01
# 82 633 3198 2851 896 1581 1732 1292 295 132
# Inhib_02 Inhib_03 Inhib_04 Inhib_05 Inhib_06 drop_01 drop_02 drop_03 drop_04
# 461 2242 6018 1311 249 11 3 2 7


sce$cellType_broad_hc <- anno_hc2$broad[match(sce$collapsedCluster, anno_hc$cluster)]
sce$cellType_hc <- anno_hc2$cellType[match(sce$collapsedCluster, anno_hc2$cluster)]

table(sce$cellType_broad_hc)
# Astro EndoMural Micro Oligo OPC Excit Inhib Ambiguous
# Astro EndoMural Micro Oligo OPC Excit Inhib Ambiguous
# 3979 2157 1601 10894 1940 24809 11067 21157

table(sce$cellType_hc)
# Astro EndoMural_01 EndoMural_02 Micro Oligo_01 Oligo_02 Oligo_03 OPC Excit_01
# 3979 446 1711 1601 1868 4732 4294 1940 7927
# Excit_02 Excit_03 Excit_04 Excit_05 Excit_06 Excit_07 Excit_08 Excit_09 Excit_10
# 2487 1309 2171 2532 329 334 1463 2561 1079
# Excit_11 Excit_12 Excit_13 Excit_14 Excit_15 Inhib_01 Inhib_02 Inhib_03 Inhib_04
# 482 420 1567 82 66 5366 1267 1310 565
# Inhib_05 Inhib_06 Ambiguous
# 1192 1367 21157
# Astro EndoMural_01 EndoMural_02 Micro Oligo_01 Oligo_02 Oligo_03 OPC Excit_01
# 3979 446 1711 1601 1868 4732 4294 1940 7927
# Excit_02 Excit_03 Excit_04 Excit_05 Excit_06 Excit_07 Excit_08 Excit_09 Excit_10
# 2487 1309 2171 2532 329 334 1463 2561 1079
# Excit_11 Excit_12 Excit_13 Excit_14 Excit_15 Inhib_01 Inhib_02 Inhib_03 Inhib_04
# 482 420 1567 82 66 5366 1267 1310 565
# Inhib_05 Inhib_06 Ambiguous
# 1192 1367 21157

## Check out prop
(prop_k <- 100 * round(table(sce$cellType_broad_k) / ncol(sce), 3))
# Astro EndoMural MicroOligo Oligo OPC Excit Inhib drop
# 4.6 1.7 7.1 43.4 2.3 27.4 13.4 0.0
# Astro EndoMural MicroOligo Oligo OPC Excit Inhib drop
# 4.6 1.7 7.1 43.4 2.3 27.4 13.4 0.0

(prop_hc <- 100 * round(table(sce$cellType_broad_hc) / ncol(sce), 3))
# Astro EndoMural Micro Oligo OPC Excit Inhib Ambiguous
# 5.1 2.8 2.1 14.0 2.5 32.0 14.3 27.3
# Astro EndoMural Micro Oligo OPC Excit Inhib Ambiguous
# 5.1 2.8 2.1 14.0 2.5 32.0 14.3 27.3

as.data.frame(prop_k) %>% full_join(as.data.frame(prop_hc) %>% rename(Freq_HC = Freq))
# Var1 Freq Freq_HC
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