Treatments#
The module treatments provides functions related to Treatments section of
cBioPortal Web Public API.
- pybioportal.treatments.fetch_all_patient_level_treatments(study_view_filter, tier='Agent')#
Fetch all patient level treatments.
- Parameters:
study_view_filter – Study view filter.
tier (str) –
Tier for treatment.
Possible values:
”Agent”: Display treatments by agent (default).
”AgentClass”: Display treatments by agent class.
”AgentTarget”: Display treatments by agent target.
- Returns:
A DataFrame containing patient treatment rows.
- Return type:
pandas.DataFrame
- pybioportal.treatments.fetch_all_sample_level_treatments(study_view_filter, tier='Agent')#
Fetch all sample level treatments.
- Parameters:
study_view_filter – Study view filter.
tier (str) –
Tier for treatment.
Possible values:
”Agent”: Display treatments by agent (default).
”AgentClass”: Display treatments by agent class.
”AgentTarget”: Display treatments by agent target.
- Returns:
A DataFrame containing sample treatment rows.
- Return type:
pandas.DataFrame
- pybioportal.treatments.fetch_status_display_patient_trts(study_ids, tier='Agent')#
Check if patient level treatments should be displayed.
- Parameters:
study_ids (list of str) – List of Study IDs.
tier (str) –
Tier for treatment.
Possible values:
”Agent”: Display treatments by agent (default).
”AgentClass”: Display treatments by agent class.
”AgentTarget”: Display treatments by agent target.
- Returns:
True if patient level treatments should be displayed, False otherwise.
- Return type:
bool
- pybioportal.treatments.fetch_status_display_sample_trts(study_ids, tier='Agent')#
Check if sample level treatments should be displayed.
- Parameters:
study_ids (list of str) – List of Study IDs.
tier (str) –
Tier for treatment.
Possible values:
”Agent”: Display treatments by agent (default).
”AgentClass”: Display treatments by agent class.
”AgentTarget”: Display treatments by agent target.
- Returns:
True if sample level treatments should be displayed, False otherwise.
- Return type:
bool
Examples#
from pybioportal import treatments as trt
Get the Study IDs of all studies
from pybioportal import studies as std
studies = std.get_all_studies(projection="DETAILED")
std_ids = studies["studyId"].to_list()
print(f"First Study IDs of {len(std_ids)}: {std_ids[0:5]}")
First Study IDs of 393: ['acc_tcga', 'laml_tcga', 'blca_tcga', 'kirc_tcga', 'cesc_tcga']
trt.fetch_status_display_patient_trts(study_ids=std_ids)
True
trt.fetch_status_display_sample_trts(study_ids=std_ids)
True
filter1a = {"studyIds": std_ids}
df1a = trt.fetch_all_patient_level_treatments(study_view_filter=filter1a)
df1a
| treatment | count | patientId | sampleId | studyId | |
|---|---|---|---|---|---|
| 0 | CCNU + thalidomide | 1 | P01 | P01_Pri | lgg_ucsf_2014 |
| 1 | CCNU + thalidomide | 1 | P01 | P01_Rec | lgg_ucsf_2014 |
| 2 | MK-3475 | 2 | P-19 | 121441-2T-19 | mel_tsam_liang_2017 |
| 3 | MK-3475 | 2 | P-17 | 101984-1T-17 | mel_tsam_liang_2017 |
| 4 | Doxorubicin HCL | 1 | HTA9_1 | HTA9_1-Bx3 | brca_hta9_htan_2022 |
| ... | ... | ... | ... | ... | ... |
| 21974 | Megestrol Acetate | 17 | TCGA-B5-A11I | TCGA-B5-A11I-01 | ucec_tcga_pan_can_atlas_2018 |
| 21975 | Megestrol Acetate | 17 | TCGA-AP-A0LL | TCGA-AP-A0LL-01 | ucec_tcga_pan_can_atlas_2018 |
| 21976 | Megestrol Acetate | 17 | TCGA-B5-A11Q | TCGA-B5-A11Q-01 | ucec_tcga_pan_can_atlas_2018 |
| 21977 | Plfe | 1 | TCGA-D7-8570 | TCGA-D7-8570-01 | stad_tcga_pan_can_atlas_2018 |
| 21978 | Ondansetron | 1 | TCGA-EB-A57M | TCGA-EB-A57M-01 | skcm_tcga_pan_can_atlas_2018 |
21979 rows × 5 columns
filter1b = {"patientTreatmentFilters": {
"filters": [
{
"filters": [
{
"treatment": "Palbociclib"
}
]
}
]
},
"studyIds": std_ids}
df1b = trt.fetch_all_patient_level_treatments(study_view_filter=filter1b)
df1b
| treatment | count | patientId | sampleId | studyId | |
|---|---|---|---|---|---|
| 0 | Doxorubicin HCL | 1 | HTA9_1 | HTA9_1-Bx3 | brca_hta9_htan_2022 |
| 1 | Doxorubicin HCL | 1 | HTA9_1 | HTA9_1-Bx4 | brca_hta9_htan_2022 |
| 2 | Doxorubicin HCL | 1 | HTA9_1 | HTA9_1-Bx1 | brca_hta9_htan_2022 |
| 3 | Doxorubicin HCL | 1 | HTA9_1 | HTA9_1-Bx2 | brca_hta9_htan_2022 |
| 4 | Doxorubicin HCL | 1 | HTA9_1 | HTA9_1-PR | brca_hta9_htan_2022 |
| ... | ... | ... | ... | ... | ... |
| 116 | Letrozole | 6 | 37916 | 37916 | pog570_bcgsc_2020 |
| 117 | Letrozole | 6 | 38725 | 38725 | pog570_bcgsc_2020 |
| 118 | Letrozole | 6 | 37844 | 37844 | pog570_bcgsc_2020 |
| 119 | Letrozole | 6 | 36621 | 36621 | pog570_bcgsc_2020 |
| 120 | Letrozole | 6 | 31509 | 31509 | pog570_bcgsc_2020 |
121 rows × 5 columns
filter2b = {"sampleTreatmentFilters": {
"filters": [
{
"filters": [
{
"time": "Pre",
"treatment": "Palbociclib"
},
{
"time": "Post",
"treatment": "Palbociclib"
}
]
}
]
},
"studyIds": ["brca_tcga"]}
df2b = trt.fetch_all_sample_level_treatments(study_view_filter=filter2b)
df2b
| time | treatment | count | patientId | sampleId | studyId | timeTaken | |
|---|---|---|---|---|---|---|---|
| 0 | Post | DOXORUBICIN | 1 | TCGA-60-2697 | TCGA-60-2697-01 | lusc_tcga_pan_can_atlas_2018 | 93 |
| 1 | Pre | pemetrexed+bevacizumab+erlotinib | 2 | MSK_LX25 | P-0000636-T01-IM3 | lung_msk_pdx | 203 |
| 2 | Pre | pemetrexed+bevacizumab+erlotinib | 2 | MSK_LX25 | MSK_LX25 | lung_msk_pdx | 203 |
| 3 | Pre | BICALUTAMIDE | 9 | MPCPROJECT_0319 | RP-1532_PCProject_0319_T1_v2_Exome_OnPrem | mpcproject_broad_2021 | 0 |
| 4 | Pre | BICALUTAMIDE | 9 | MPCPROJECT_0130 | RP-1532_PCProject_0130_T1_v3_Exome_OnPrem | mpcproject_broad_2021 | 0 |
| ... | ... | ... | ... | ... | ... | ... | ... |
| 12784 | Pre | Vemurafenib | 11 | TCGA-GN-A4U7 | TCGA-GN-A4U7-06 | skcm_tcga_pan_can_atlas_2018 | 163 |
| 12785 | Pre | TARCEVA/ERLOTINIB | 1 | TCGA-18-3412 | TCGA-18-3412-01 | lusc_tcga_pan_can_atlas_2018 | 0 |
| 12786 | Pre | CPT-11 | 1 | TCGA-38-4632 | TCGA-38-4632-01 | luad_tcga_pan_can_atlas_2018 | 0 |
| 12787 | Pre | ZOLEDRONIC ACID | 1 | MPCPROJECT_0031 | RP-1532_PCProject_0031_T1_v2_Exome_OnPrem | mpcproject_broad_2021 | 0 |
| 12788 | Post | carboplatin+pemetrexed (maintenance) +bevacizumab | 1 | MSK_LX301 | MSK_LX301B | lung_msk_pdx | 1786 |
12789 rows × 7 columns