main, step 1 and step 2 pages text refined

Author: mabraao

docs/index.html

@@ -1,115 +1,115 @@
 CellType
-0,Fibroblast
+0,Mesenchymal_cells
 1,NA
-2,Fibroblast
-3,T
-4,T
-5,Endothelial
-6,Endothelial
-7,T
-8,Fibroblast
+2,Mesenchymal_cells
+3,T/NK
+4,T/NK
+5,Endothelial_cells
+6,Endothelial_cells
+7,T/NK
+8,Mesenchymal_cells
 9,NA
-10,Fibroblast
-11,T
-12,Fibroblast
-13,Fibroblast
-14,T
+10,Mesenchymal_cells
+11,T/NK
+12,Mesenchymal_cells
+13,Mesenchymal_cells
+14,T/NK
 15,NA
-16,Smooth
-17,Fibroblast
-18,T
-19,Fibroblast
-20,Myeloid
-21,Fibroblast
-22,T
-23,Fibroblast
-24,Myeloid
-25,T
-26,Fibroblast
-27,Epithelial
-28,T
-29,Plasma
-30,Fibroblast
-31,Fibroblast
-32,T
-33,T
-34,Fibroblast
-35,Fibroblast
-36,Smooth
-37,T
+16,Smooth_Muscle_cells
+17,Mesenchymal_cells
+18,T/NK
+19,Mesenchymal_cells
+20,Myeloid_cells
+21,Mesenchymal_cells
+22,T/NK
+23,Mesenchymal_cells
+24,Myeloid_cells
+25,T/NK
+26,Mesenchymal_cells
+27,Epithelial_cells
+28,T/NK
+29,B/Plasma_cells
+30,Mesenchymal_cells
+31,Mesenchymal_cells
+32,T/NK
+33,T/NK
+34,Mesenchymal_cells
+35,Mesenchymal_cells
+36,Smooth_Muscle_cells
+37,T/NK
 38,Erythrocytes
-39,Myeloid
-40,Fibroblast
-41,Plasma
-42,Myeloid
-43,NA
-44,Fibroblast
-45,Fibroblast
+39,Myeloid_cells
+40,Mesenchymal_cells
+41,B/Plasma_cells
+42,Myeloid_cells
+43,Epithelial_cells
+44,Mesenchymal_cells
+45,Mesenchymal_cells
 46,NA
-47,Fibroblast
-48,Fibroblast
-49,Endothelial
-50,Myeloid
-51,Smooth
-52,Epithelial
-53,Myeloid
-54,Fibroblast
-55,Epithelial
-56,T
-57,Fibroblast
-58,Fibroblast
-59,Fibroblast
-60,Myeloid
-61,T
-62,Epithelial
-63,NA
-64,Fibroblast
-65,Epithelial
-66,Smooth
-67,NA
-68,Mast
+47,Mesenchymal_cells
+48,Mesenchymal_cells
+49,Endothelial_cells
+50,Myeloid_cells
+51,Smooth_Muscle_cells
+52,Epithelial_cells
+53,Epithelial_cells
+54,Epithelial_cells
+55,Epithelial_cells
+56,T/NK
+57,Epithelial_cells
+58,Mesenchymal_cells
+59,Mesenchymal_cells
+60,Myeloid_cells
+61,T/NK
+62,Epithelial_cells
+63,Epithelial_cells
+64,Mesenchymal_cells
+65,Epithelial_cells
+66,Smooth_Muscle_cells
+67,Epithelial_cells
+68,Mast_cells
 69,Erythrocytes
-70,Myeloid
-71,Fibroblast
-72,T
-73,T
-74,Fibroblast
-75,Fibroblast
-76,Fibroblast
-77,T
-78,Myeloid
-79,Epithelial
-80,T
-81,T
+70,Myeloid_cells
+71,Epithelial_cells
+72,T/NK
+73,T/NK
+74,Mesenchymal_cells
+75,Mesenchymal_cells
+76,Mesenchymal_cells
+77,T/NK
+78,T/NK
+79,Epithelial_cells
+80,T/NK
+81,T/NK
 82,Erythrocytes
-83,Fibroblast
-84,Myeloid
-85,Plasma
-86,Smooth
-87,Fibroblast
-88,Epithelial
-89,T
-90,Endothelial
-91,Myeloid
-92,T
-93,T
-94,T
-95,Endothelial
-96,T
+83,Mesenchymal_cells
+84,Myeloid_cells
+85,B/Plasma_cells
+86,Smooth_Muscle_cells
+87,Mesenchymal_cells
+88,Epithelial_cells
+89,T/NK
+90,Endothelial_cells
+91,Myeloid_cells
+92,T/NK
+93,T/NK
+94,T/NK
+95,Endothelial_cells
+96,T/NK
 97,Erythrocytes
-98,Fibroblast
-99,Endothelial
-100,Fibroblast
+98,Epithelial_cells
+99,Endothelial_cells
+100,Epithelial_cells
 101,NA
-102,Myeloid
-103,Fibroblast
-104,T
-105,T
-106,Smooth
-107,T
-108,Myeloid
-109,Fibroblast
-110,Endothelial
-111,NA
-112,Smooth
+102,Myeloid_cells
+103,Mesenchymal_cells
+104,T/NK
+105,T/NK
+106,Epithelial_cells
+107,T/NK
+108,Myeloid_cells
+109,Mesenchymal_cells
+110,Endothelial_cells
+111,Epithelial_cells
+112,Smooth_Muscle_cells
 113,NA

docs/step1.html

@@ -13,7 +13,7 @@ SUPERvised single Cell Annotation Tool
 
 ### Introduction
 
-This document contains code workflows, explaining how to perform the bioinformatics analysis described in ***A single-cell transcriptomic analysis of endometriosis, endometriomas, eutopic endometrial samples and uninvolved ovary tissues highlights cell populations characteristic of these tissue types. Transcriptional and cellular heterogeneity across tissues suggests novel therapeutic targets and biomarkers for this disease.***
+This document contains code workflows, explaining how to perform the cell annotation procedures for the single cell analyses described in ***A single-cell transcriptomic analysis of endometriosis, endometriomas, eutopic endometrial samples and uninvolved ovary tissues highlights cell populations characteristic of these tissue types. Transcriptional and cellular heterogeneity across tissues suggests novel therapeutic targets and biomarkers for this disease.***
 
 ### Authors
 
@@ -24,8 +24,9 @@ Marcos A.S. Fonseca\*, Marcela Haro\*, Kelly N. Wright\*, Xianzhi Lin\*, Forough
 
 #### Workflow for cell annotation
 
+Please navigate to the document tabs above to acess the procedures in `step 1` and `step 2` for the single cell cluster annotations
 
-``` {r message=F, echo=FALSE, warning=F, fig.align='center', out.width = "80%"}
+``` {r message=F, echo=FALSE, warning=F, fig.align='center', out.width = "70%"}
 img1_path = "img/annot_workflow.pdf-1.png"
 include_graphics(img1_path)