antunderwood

"DATE","PRCP","TMAX","TMIN","RAIN"
"1948-01-01",0.47,51,42,"TRUE"
"1948-01-02",0.59,45,36,"TRUE"
"1948-01-03",0.42,45,35,"TRUE"
"1948-01-04",0.31,45,34,"TRUE"
"1948-01-05",0.17,45,32,"TRUE"
"1948-01-06",0.44,48,39,"TRUE"
"1948-01-07",0.41,50,40,"TRUE"
"1948-01-08",0.04,48,35,"TRUE"
"1948-01-09",0.12,50,31,"TRUE"

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{
  "directed": true,
  "graph": {},
  "links": [
    {
      "coverage": 1.0,
      "identity": 0.997,
      "source": "card:ARO:3000005",
      "target": "ncbi:WP_063856692.1",

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ROW_IDX	COUNTRY_A	LABORATORY	ORIGIN	PATIENT_ID	LAST_NAME	FIRST_NAME	SEX	DATE_BIRTH	AGE	PAT_TYPE	WARD	INSTITUT	DEPARTMENT	WARD_TYPE	DATE_ADMIS	SPEC_NUM	SPEC_DATE	SPEC_TYPE	LOCAL_SPEC	SPEC_CODE	SPEC_REAS	ISOL_NUM	ORGANISM	LOCAL_ORG	ORG_TYPE	SEROTYPE	MRSA	VRE	BETA_LACT	ESBL	CARBAPENEM	MRSA_SCRN	INDUC_CLI	COMMENT	DATE_DATA	AMC_NM	AMK_NM	AMP_NM	ATM_NM	AZM_NM	CAZ_NM	CEP_NM	CFM_NM	CHL_NM	CIP_NM	CLI_NM	COL_NM	COP_NM	CRO_NM	CSL_NM	CTX_NM	CXA_NM	CXM_NM	CZO_NM	DAP_NM	DOR_NM	ENR_NM	ERY_NM	ETP_NM	FEP_NM	FOX_NM	GEN_NM	IPM_NM	LNZ_NM	LVX_NM	MAN_NM	MEM_NM	MFX_NM	MNO_NM	NAL_NM	NOR_NM	NTZ_NM	OFX_NM	OXA_NM	PEN_NM	PIP_NM	QDA_NM	RIF_NM	SAM_NM	SPT_NM	STR_NM	SXT_NM	TCC_NM	TCY_NM	TEC_NM	TGC_NM	TOB_NM	TZP_NM	VAN_NM
0.00000	COL	RET		G18000002												RB 141							eco	eco	-										2020-09-30		16				16				>2			<=0.5	>32							<=0.12			<=0.5	8	16	>8	<=0.25				<=0.25												>16							<=0.5		8	

antunderwood

---
title: "Plotting stacked AST/AMR data"
output: html_notebook
---

Read in some data. I've used JSON so I can have the data in this text file
```{r message=FALSE, warning=FALSE}
library(jsonlite)
ast_gene_json <- '[
  {