replaced knitrwith kableExtra

tutorials/Tutorial_Metadata_JSON.qmd

@@ -95,7 +95,6 @@ For further information on readability of spreadsheets, see the [Six tips for be
 
 library("dplyr") # data operations
 library("kableExtra") # for rendering of tables in HTML or PDF
-library("knitr") # rendering of the report
 
 ```
 
@@ -122,7 +121,7 @@ Let's take a look:
 ```{r view-table}
 #| echo: false
 
-knitr::kable(metadata) %>%
+kableExtra::kable(metadata) %>%
   scroll_box(height= "300px")
 
 ```
@@ -180,6 +179,7 @@ This is all the code that you'll need to execute what we talked about in this tu
 ```{r}
 #| code-fold: show
 #| output: false
+
 <<dummy-metadata>>
 <<make-json>>
 ```
@@ -264,7 +264,6 @@ Let's start by creating the dummy experimental dataset:
 library("dplyr") # data operations
 library("jsonlite") # creation of JSON files
 library("kableExtra") # for rendering of tables in HTML or PDF
-library("knitr") # rendering of the report
 library("readr")  #I/O
 ```
 
@@ -376,7 +375,7 @@ Before we proceed with creating JSON files, let's take a look at the various tab
 ```{r show-JSON-tab}
 #| echo: false
 # check 
-knitr::kable(json_fields) %>%
+kableExtra::kable(json_fields) %>%
   scroll_box(height= "300px")
 
 ```
@@ -386,7 +385,7 @@ knitr::kable(json_fields) %>%
 ```{r show-metadata}
 #| echo: false
 # check 
-knitr::kable(subj_info) %>%
+kableExtra::kable(subj_info) %>%
   scroll_box(height= "300px")
 
 ```
@@ -396,7 +395,7 @@ knitr::kable(subj_info) %>%
 ```{r show-filenames}
 #| echo: false
 # check 
-knitr::kable(files_tib) %>%
+kableExtra::kable(files_tib) %>%
   scroll_box(height= "300px")
 
 ```
@@ -522,3 +521,4 @@ This is all the code that you'll need to execute what we talked about in this tu
 
 
 
+

tutorials/Tutorial_Metadata_JSON/experiment_results/dummyExp_metadata.csv

 id,img_location,sex,condition,treatment
-subject_88,./Tutorial_Metadata_JSON/experiment_results/imaging/subject_88_imgfile.tiff,male,B,treat_3
-subject_86,./Tutorial_Metadata_JSON/experiment_results/imaging/subject_86_imgfile.tiff,male,A,treat_2
-subject_95,./Tutorial_Metadata_JSON/experiment_results/imaging/subject_95_imgfile.tiff,male,B,control
-subject_59,./Tutorial_Metadata_JSON/experiment_results/imaging/subject_59_imgfile.tiff,female,B,treat_2
-subject_90,./Tutorial_Metadata_JSON/experiment_results/imaging/subject_90_imgfile.tiff,female,A,treat_3
-subject_53,./Tutorial_Metadata_JSON/experiment_results/imaging/subject_53_imgfile.tiff,male,B,treat_2
-subject_58,./Tutorial_Metadata_JSON/experiment_results/imaging/subject_58_imgfile.tiff,female,A,control
-subject_46,./Tutorial_Metadata_JSON/experiment_results/imaging/subject_46_imgfile.tiff,male,B,treat_2
-subject_56,./Tutorial_Metadata_JSON/experiment_results/imaging/subject_56_imgfile.tiff,male,B,control
-subject_100,./Tutorial_Metadata_JSON/experiment_results/imaging/subject_100_imgfile.tiff,male,B,treat_1
+subject_28,./Tutorial_Metadata_JSON/experiment_results/imaging/subject_28_imgfile.tiff,male,A,treat_2
+subject_21,./Tutorial_Metadata_JSON/experiment_results/imaging/subject_21_imgfile.tiff,female,A,treat_3
+subject_16,./Tutorial_Metadata_JSON/experiment_results/imaging/subject_16_imgfile.tiff,female,B,treat_3
+subject_81,./Tutorial_Metadata_JSON/experiment_results/imaging/subject_81_imgfile.tiff,female,A,control
+subject_25,./Tutorial_Metadata_JSON/experiment_results/imaging/subject_25_imgfile.tiff,male,B,control
+subject_14,./Tutorial_Metadata_JSON/experiment_results/imaging/subject_14_imgfile.tiff,male,A,control
+subject_31,./Tutorial_Metadata_JSON/experiment_results/imaging/subject_31_imgfile.tiff,male,B,treat_1
+subject_86,./Tutorial_Metadata_JSON/experiment_results/imaging/subject_86_imgfile.tiff,female,B,control
+subject_38,./Tutorial_Metadata_JSON/experiment_results/imaging/subject_38_imgfile.tiff,female,B,treat_3
+subject_67,./Tutorial_Metadata_JSON/experiment_results/imaging/subject_67_imgfile.tiff,male,A,treat_2

tutorials/Tutorial_Metadata_JSON/experiment_results/imaging/subject_100_imgfile.json

@@ -9,7 +9,7 @@
   "masking": "methodX",
   "counting": "algoY",
   "subjectID": "subject_100",
-  "sex": "male",
+  "sex": "female",
   "condition": "B",
-  "treatment": "treat_1"
+  "treatment": "treat_2"
 }

tutorials/Tutorial_Metadata_JSON/experiment_results/imaging/subject_10_imgfile.json

+{
+  "lab_name": "labA",
+  "plant_species": "Populus trichocarpa",
+  "tissue_type": "Shoot apical meristem",
+  "microscope_model": "brandX ABCmicro",
+  "magnification": "30",
+  "filter": "filterA123",
+  "binning": "FALSE",
+  "masking": "methodX",
+  "counting": "algoY",
+  "subjectID": "subject_10",
+  "sex": "male",
+  "condition": "A",
+  "treatment": "treat_1"
+}

tutorials/Tutorial_Metadata_JSON/experiment_results/imaging/subject_12_imgfile.json

+{
+  "lab_name": "labA",
+  "plant_species": "Populus trichocarpa",
+  "tissue_type": "Shoot apical meristem",
+  "microscope_model": "brandX ABCmicro",
+  "magnification": "30",
+  "filter": "filterA123",
+  "binning": "FALSE",
+  "masking": "methodX",
+  "counting": "algoY",
+  "subjectID": "subject_12",
+  "sex": "female",
+  "condition": "B",
+  "treatment": "control"
+}

tutorials/Tutorial_Metadata_JSON/experiment_results/imaging/subject_13_imgfile.json

@@ -9,7 +9,7 @@
   "masking": "methodX",
   "counting": "algoY",
   "subjectID": "subject_13",
-  "sex": "male",
+  "sex": "female",
   "condition": "A",
   "treatment": "treat_3"
 }

tutorials/Tutorial_Metadata_JSON/experiment_results/imaging/subject_14_imgfile.json

+{
+  "lab_name": "labA",
+  "plant_species": "Populus trichocarpa",
+  "tissue_type": "Shoot apical meristem",
+  "microscope_model": "brandX ABCmicro",
+  "magnification": "30",
+  "filter": "filterA123",
+  "binning": "FALSE",
+  "masking": "methodX",
+  "counting": "algoY",
+  "subjectID": "subject_14",
+  "sex": "male",
+  "condition": "A",
+  "treatment": "control"
+}

tutorials/Tutorial_Metadata_JSON/experiment_results/imaging/subject_16_imgfile.json

+{
+  "lab_name": "labA",
+  "plant_species": "Populus trichocarpa",
+  "tissue_type": "Shoot apical meristem",
+  "microscope_model": "brandX ABCmicro",
+  "magnification": "30",
+  "filter": "filterA123",
+  "binning": "FALSE",
+  "masking": "methodX",
+  "counting": "algoY",
+  "subjectID": "subject_16",
+  "sex": "female",
+  "condition": "B",
+  "treatment": "treat_3"
+}

tutorials/Tutorial_Metadata_JSON/experiment_results/imaging/subject_1_imgfile.json

+{
+  "lab_name": "labA",
+  "plant_species": "Populus trichocarpa",
+  "tissue_type": "Shoot apical meristem",
+  "microscope_model": "brandX ABCmicro",
+  "magnification": "30",
+  "filter": "filterA123",
+  "binning": "FALSE",
+  "masking": "methodX",
+  "counting": "algoY",
+  "subjectID": "subject_1",
+  "sex": "male",
+  "condition": "A",
+  "treatment": "control"
+}

tutorials/Tutorial_Metadata_JSON/experiment_results/imaging/subject_21_imgfile.json

+{
+  "lab_name": "labA",
+  "plant_species": "Populus trichocarpa",
+  "tissue_type": "Shoot apical meristem",
+  "microscope_model": "brandX ABCmicro",
+  "magnification": "30",
+  "filter": "filterA123",
+  "binning": "FALSE",
+  "masking": "methodX",
+  "counting": "algoY",
+  "subjectID": "subject_21",
+  "sex": "female",
+  "condition": "A",
+  "treatment": "treat_3"
+}

tutorials/Tutorial_Metadata_JSON/experiment_results/imaging/subject_25_imgfile.json

+{
+  "lab_name": "labA",
+  "plant_species": "Populus trichocarpa",
+  "tissue_type": "Shoot apical meristem",
+  "microscope_model": "brandX ABCmicro",
+  "magnification": "30",
+  "filter": "filterA123",
+  "binning": "FALSE",
+  "masking": "methodX",
+  "counting": "algoY",
+  "subjectID": "subject_25",
+  "sex": "male",
+  "condition": "B",
+  "treatment": "control"
+}

tutorials/Tutorial_Metadata_JSON/experiment_results/imaging/subject_28_imgfile.json

+{
+  "lab_name": "labA",
+  "plant_species": "Populus trichocarpa",
+  "tissue_type": "Shoot apical meristem",
+  "microscope_model": "brandX ABCmicro",
+  "magnification": "30",
+  "filter": "filterA123",
+  "binning": "FALSE",
+  "masking": "methodX",
+  "counting": "algoY",
+  "subjectID": "subject_28",
+  "sex": "male",
+  "condition": "A",
+  "treatment": "treat_2"
+}