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AlexsLemonade / OpenPBTA-analysis

The analysis repository for the Open Pediatric Brain Tumor Atlas Project
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Updates required post v22 histologies file release #1368

Closed jharenza closed 2 years ago

jharenza commented 2 years ago

Per my comments on #1365, some LGG cancer_group updates were implemented, but never transferred to pbta-histologies.tsv. This resulted in separate cancer_group in plots for Low-grade glioma astrocytoma (LGGA) and ganglioglioma but not PXA, pilocytic, and SEGA because they remained within LGGA:

# v21 rna
v21 %>%
  filter((short_histology == "LGAT" | short_histology == "Ganglioglioma") & experimental_strategy == "RNA-Seq") %>%
  select(cancer_group, tumor_descriptor) %>%
  table()
                                     tumor_descriptor
cancer_group                          Initial CNS Tumor Progressive Recurrence Second Malignancy
  Ganglioglioma                                      36           8          3                 0
  Low-grade glioma astrocytoma                      200          31         12                 1
  Pilocytic astrocytoma                               0           1          0                 0
  Pleomorphic xanthoastrocytoma                       2           0          0                 0
  Subependymal Giant Cell Astrocytoma                 3           1          0                 0

#v22 rna
histology %>%
  filter((short_histology == "LGAT" | short_histology == "Ganglioglioma") & experimental_strategy == "RNA-Seq") %>%
  select(cancer_group, tumor_descriptor) %>%
  table()
                                     tumor_descriptor
cancer_group                          Initial CNS Tumor Progressive Recurrence Second Malignancy
  Diffuse fibrillary astrocytoma                      5           0          1                 0
  Ganglioglioma                                      36           8          3                 0
  Gliomatosis cerebri                                 1           0          0                 0
  Low-grade glioma astrocytoma                       72          16          6                 0
  Oligodendroglioma                                   1           0          0                 0
  Pilocytic astrocytoma                             106          15          4                 1
  Pleomorphic xanthoastrocytoma                       9           1          1                 0
  Subependymal Giant Cell Astrocytoma                11           1          0                 0

#v21 dna 
v21 %>%
  filter((short_histology == "LGAT" | short_histology == "Ganglioglioma") & experimental_strategy != "RNA-Seq") %>%
  select(cancer_group, tumor_descriptor) %>%
  table()
                                     tumor_descriptor
cancer_group                          Initial CNS Tumor Progressive Recurrence Second Malignancy
  Diffuse fibrillary astrocytoma                      1           0          0                 0
  Ganglioglioma                                      35          10          3                 0
  Low-grade glioma astrocytoma                      190          30         13                 1
  Pilocytic astrocytoma                               1           1          0                 0
  Pleomorphic xanthoastrocytoma                       1           0          0                 0
  Subependymal Giant Cell Astrocytoma                 2           1          0                 0

#v22 dna
histology %>%
  filter((short_histology == "LGAT" | short_histology == "Ganglioglioma") & experimental_strategy != "RNA-Seq") %>%
  select(cancer_group, tumor_descriptor) %>%
  table()
                                     tumor_descriptor
cancer_group                          Initial CNS Tumor Progressive Recurrence Second Malignancy
  Diffuse fibrillary astrocytoma                      5           0          1                 0
  Ganglioglioma                                      35          10          3                 0
  Gliomatosis cerebri                                 1           0          0                 0
  Low-grade glioma astrocytoma                       67          16          6                 0
  Oligodendroglioma                                   1           0          0                 0
  Pilocytic astrocytoma                             101          14          5                 1
  Pleomorphic xanthoastrocytoma                       9           1          1                 0
  Subependymal Giant Cell Astrocytoma                11           1          0                 0

Therefore, sadly, we will need to update some modules and figures with the v22 histology file cancer group mappings and it looks like we will need additional colors for Pilocytic astrocytoma, Subependymal Giant Cell Astrocytoma, and possibly Pleomorphic xanthoastrocytoma if we have modules using > Initial CNS Tumor (chromothripsis looks to be one of these).

Color codes to be generated

Figures to rerun/replace and modules

Tables to replace and modules

jharenza commented 2 years ago

Noting that the remaining to-dos are in PR now and this can be closed when #1448, #1458, #1515, and #1519 are merged

jharenza commented 2 years ago

Closing in favor of #1487 tracking figures now